Multiple sequence alignment - TraesCS4A01G333100

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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 TraesCS4A01G333100 chr4A 100.000 4513 0 0 1 4513 616904264 616899752 0.000000e+00 8335.0
1 TraesCS4A01G333100 chr4A 82.009 428 51 11 3020 3430 616869237 616868819 1.550000e-89 340.0
2 TraesCS4A01G333100 chr4A 77.132 516 100 15 1003 1512 625542294 625542797 2.660000e-72 283.0
3 TraesCS4A01G333100 chr4A 76.655 287 57 8 1874 2152 616608607 616608323 2.810000e-32 150.0
4 TraesCS4A01G333100 chr4A 85.965 114 16 0 1043 1156 616674955 616674842 6.130000e-24 122.0
5 TraesCS4A01G333100 chr4A 93.651 63 4 0 2929 2991 616869305 616869243 1.340000e-15 95.3
6 TraesCS4A01G333100 chr5D 94.107 2189 95 20 2338 4513 551052676 551054843 0.000000e+00 3297.0
7 TraesCS4A01G333100 chr5D 93.434 929 28 14 660 1564 551051389 551052308 0.000000e+00 1347.0
8 TraesCS4A01G333100 chr5D 85.269 353 26 6 272 623 551051069 551051396 1.550000e-89 340.0
9 TraesCS4A01G333100 chr5D 76.157 562 106 23 979 1519 543508821 543508267 2.070000e-68 270.0
10 TraesCS4A01G333100 chr5D 76.471 527 101 15 998 1515 543465646 543465134 9.630000e-67 265.0
11 TraesCS4A01G333100 chr5D 76.426 526 103 18 1006 1517 551447709 551448227 9.630000e-67 265.0
12 TraesCS4A01G333100 chr5D 91.848 184 13 1 47 230 551050880 551051061 5.790000e-64 255.0
13 TraesCS4A01G333100 chr5D 82.581 310 34 8 3166 3472 551082893 551083185 5.790000e-64 255.0
14 TraesCS4A01G333100 chr5D 75.964 337 71 8 1824 2152 551754598 551754932 1.000000e-36 165.0
15 TraesCS4A01G333100 chr5D 96.104 77 1 1 2244 2320 551052616 551052690 1.700000e-24 124.0
16 TraesCS4A01G333100 chr5B 90.950 1547 78 15 696 2189 703329652 703331189 0.000000e+00 2025.0
17 TraesCS4A01G333100 chr5B 95.542 673 27 3 2192 2863 703335382 703336052 0.000000e+00 1074.0
18 TraesCS4A01G333100 chr5B 95.563 293 11 2 332 623 703329209 703329500 6.840000e-128 468.0
19 TraesCS4A01G333100 chr5B 81.881 436 52 15 3014 3431 699386730 699387156 4.320000e-90 342.0
20 TraesCS4A01G333100 chr5B 94.845 194 7 3 155 347 703329002 703329193 2.640000e-77 300.0
21 TraesCS4A01G333100 chr5B 76.863 510 92 21 1024 1517 700237572 700237073 9.630000e-67 265.0
22 TraesCS4A01G333100 chr5B 75.184 544 109 21 979 1515 685257219 685256695 2.710000e-57 233.0
23 TraesCS4A01G333100 chr5B 78.824 340 67 5 1843 2179 703717021 703717358 1.630000e-54 224.0
24 TraesCS4A01G333100 chr5B 74.719 534 116 14 983 1507 703634096 703634619 2.110000e-53 220.0
25 TraesCS4A01G333100 chr5B 71.825 504 118 20 1024 1512 703502053 703501559 6.130000e-24 122.0
26 TraesCS4A01G333100 chr5B 84.444 135 7 5 6 137 703323350 703323473 2.210000e-23 121.0
27 TraesCS4A01G333100 chr1D 84.387 538 60 18 3888 4415 423303101 423302578 1.450000e-139 507.0
28 TraesCS4A01G333100 chr1A 86.026 229 25 6 3920 4144 519339543 519339318 5.830000e-59 239.0
29 TraesCS4A01G333100 chr2A 86.667 150 18 2 1024 1172 31041734 31041882 1.000000e-36 165.0


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 TraesCS4A01G333100 chr4A 616899752 616904264 4512 True 8335.0 8335 100.0000 1 4513 1 chr4A.!!$R3 4512
1 TraesCS4A01G333100 chr4A 625542294 625542797 503 False 283.0 283 77.1320 1003 1512 1 chr4A.!!$F1 509
2 TraesCS4A01G333100 chr5D 551050880 551054843 3963 False 1072.6 3297 92.1524 47 4513 5 chr5D.!!$F4 4466
3 TraesCS4A01G333100 chr5D 543508267 543508821 554 True 270.0 270 76.1570 979 1519 1 chr5D.!!$R2 540
4 TraesCS4A01G333100 chr5D 543465134 543465646 512 True 265.0 265 76.4710 998 1515 1 chr5D.!!$R1 517
5 TraesCS4A01G333100 chr5D 551447709 551448227 518 False 265.0 265 76.4260 1006 1517 1 chr5D.!!$F2 511
6 TraesCS4A01G333100 chr5B 703335382 703336052 670 False 1074.0 1074 95.5420 2192 2863 1 chr5B.!!$F3 671
7 TraesCS4A01G333100 chr5B 703329002 703331189 2187 False 931.0 2025 93.7860 155 2189 3 chr5B.!!$F6 2034
8 TraesCS4A01G333100 chr5B 685256695 685257219 524 True 233.0 233 75.1840 979 1515 1 chr5B.!!$R1 536
9 TraesCS4A01G333100 chr5B 703634096 703634619 523 False 220.0 220 74.7190 983 1507 1 chr5B.!!$F4 524
10 TraesCS4A01G333100 chr1D 423302578 423303101 523 True 507.0 507 84.3870 3888 4415 1 chr1D.!!$R1 527

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
136 137 0.313672 GATTCCAACACGCTGCCAAA 59.686 50.0 0.00 0.0 0.00 3.28 F
1001 1176 0.106217 CCTCGCCCCCAAAATACCAT 60.106 55.0 0.00 0.0 0.00 3.55 F
1760 1991 0.246635 TACGACTTGGGCTCTCAAGC 59.753 55.0 9.28 0.0 45.77 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1810 2041 0.396417 AGCATAGAGGAGCCGTCACT 60.396 55.0 0.00 0.0 0.00 3.41 R
2147 2378 0.315568 AAGACACAGAGACGCACCTC 59.684 55.0 0.00 0.0 0.00 3.85 R
3575 3844 0.319728 GGAGAGCTGACAGCAAGACA 59.680 55.0 28.43 0.0 45.56 3.41 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
21 22 3.539604 GAGGCTTTCATACAGCATCAGT 58.460 45.455 1.88 0.00 45.41 3.41
22 23 3.276857 AGGCTTTCATACAGCATCAGTG 58.723 45.455 0.00 0.00 39.21 3.66
23 24 3.054875 AGGCTTTCATACAGCATCAGTGA 60.055 43.478 0.00 0.00 39.21 3.41
24 25 3.691118 GGCTTTCATACAGCATCAGTGAA 59.309 43.478 0.00 0.00 39.21 3.18
25 26 4.201891 GGCTTTCATACAGCATCAGTGAAG 60.202 45.833 0.00 0.00 39.21 3.02
26 27 4.633126 GCTTTCATACAGCATCAGTGAAGA 59.367 41.667 0.00 0.00 37.22 2.87
27 28 5.296283 GCTTTCATACAGCATCAGTGAAGAT 59.704 40.000 0.00 0.00 37.22 2.40
28 29 6.481313 GCTTTCATACAGCATCAGTGAAGATA 59.519 38.462 0.00 0.00 37.22 1.98
29 30 7.172875 GCTTTCATACAGCATCAGTGAAGATAT 59.827 37.037 0.00 0.00 37.22 1.63
30 31 9.702494 CTTTCATACAGCATCAGTGAAGATATA 57.298 33.333 0.00 0.00 31.28 0.86
32 33 9.866798 TTCATACAGCATCAGTGAAGATATATC 57.133 33.333 4.42 4.42 0.00 1.63
33 34 9.028284 TCATACAGCATCAGTGAAGATATATCA 57.972 33.333 15.08 0.00 0.00 2.15
34 35 9.649167 CATACAGCATCAGTGAAGATATATCAA 57.351 33.333 15.08 0.00 0.00 2.57
36 37 8.774890 ACAGCATCAGTGAAGATATATCAATC 57.225 34.615 15.08 12.29 0.00 2.67
37 38 8.373220 ACAGCATCAGTGAAGATATATCAATCA 58.627 33.333 15.08 14.48 0.00 2.57
38 39 9.384764 CAGCATCAGTGAAGATATATCAATCAT 57.615 33.333 18.58 9.40 30.98 2.45
39 40 9.602568 AGCATCAGTGAAGATATATCAATCATC 57.397 33.333 18.58 13.84 30.98 2.92
40 41 9.379791 GCATCAGTGAAGATATATCAATCATCA 57.620 33.333 18.58 10.78 32.70 3.07
43 44 9.924650 TCAGTGAAGATATATCAATCATCAGTG 57.075 33.333 18.58 19.60 46.54 3.66
83 84 4.338964 TGTAGTGTTGACTCTGAAACGGTA 59.661 41.667 0.00 0.00 33.21 4.02
91 92 3.752222 GACTCTGAAACGGTAGAGAGACA 59.248 47.826 14.08 0.00 42.34 3.41
101 102 4.696402 ACGGTAGAGAGACAGTAGAGTTTG 59.304 45.833 0.00 0.00 0.00 2.93
113 114 5.163703 ACAGTAGAGTTTGTCGATGCTCTAG 60.164 44.000 14.24 9.17 40.08 2.43
127 128 3.959573 GCTCTAGCATGATTCCAACAC 57.040 47.619 0.00 0.00 41.59 3.32
131 132 0.806868 AGCATGATTCCAACACGCTG 59.193 50.000 0.00 0.00 0.00 5.18
136 137 0.313672 GATTCCAACACGCTGCCAAA 59.686 50.000 0.00 0.00 0.00 3.28
252 253 1.814429 TTTGTGAGAAGGACCCCAGA 58.186 50.000 0.00 0.00 0.00 3.86
260 261 4.410228 TGAGAAGGACCCCAGATTATCTTG 59.590 45.833 0.00 0.00 0.00 3.02
288 289 1.630148 CAGCGGGAGTCTAACTTTCG 58.370 55.000 0.00 0.00 0.00 3.46
390 422 5.531122 ACATATAACGCTCCAGCTAAAGA 57.469 39.130 0.00 0.00 39.32 2.52
416 448 8.037166 AGATTTTATGATGAAAGGCCAAGAAAC 58.963 33.333 5.01 0.00 0.00 2.78
418 450 1.885887 TGATGAAAGGCCAAGAAACCG 59.114 47.619 5.01 0.00 0.00 4.44
419 451 2.159382 GATGAAAGGCCAAGAAACCGA 58.841 47.619 5.01 0.00 0.00 4.69
503 536 9.140286 TGTAATTTCAGAGATTTACGAAGAGTG 57.860 33.333 0.00 0.00 0.00 3.51
521 554 9.893305 CGAAGAGTGTATTTAAAATCAGGTTTT 57.107 29.630 0.00 0.00 42.47 2.43
582 615 5.220322 GCAAAACAACAAAAACTAGGGAACG 60.220 40.000 0.00 0.00 0.00 3.95
604 637 5.107259 ACGCAAAACTTCAGTTTGGTTTTTC 60.107 36.000 5.70 0.00 46.47 2.29
720 755 7.452880 TGTAGGATGTTGAGGATTTGAAAAG 57.547 36.000 0.00 0.00 0.00 2.27
721 756 7.230747 TGTAGGATGTTGAGGATTTGAAAAGA 58.769 34.615 0.00 0.00 0.00 2.52
763 798 8.647143 AACATGCCTGAAATATTTATTTTCCG 57.353 30.769 0.00 0.00 36.13 4.30
796 961 8.653984 TTCATTTGTTTGAAATTATCGTCGAG 57.346 30.769 0.00 0.00 32.82 4.04
810 975 3.511699 TCGTCGAGAAAATCCTCATGTG 58.488 45.455 0.00 0.00 32.86 3.21
863 1033 0.617413 AATCTCACTGCCACTCTGGG 59.383 55.000 0.00 0.00 38.19 4.45
913 1083 2.996444 GGTTGAACCGAACCGAACT 58.004 52.632 0.00 0.00 36.28 3.01
952 1127 1.304464 CCAGGCTCAACCCTTTCCC 60.304 63.158 0.00 0.00 40.58 3.97
996 1171 1.157513 AAACCCTCGCCCCCAAAAT 59.842 52.632 0.00 0.00 0.00 1.82
997 1172 0.410270 AAACCCTCGCCCCCAAAATA 59.590 50.000 0.00 0.00 0.00 1.40
1000 1175 1.304952 CCTCGCCCCCAAAATACCA 59.695 57.895 0.00 0.00 0.00 3.25
1001 1176 0.106217 CCTCGCCCCCAAAATACCAT 60.106 55.000 0.00 0.00 0.00 3.55
1033 1227 1.299648 GTACCATGGCTGCCAGACA 59.700 57.895 27.20 0.85 37.84 3.41
1156 1351 2.107141 GATTCCGCAGCCGCTACT 59.893 61.111 0.00 0.00 35.30 2.57
1176 1371 1.629861 TGTGAGTTCCATGGAGATGCA 59.370 47.619 15.53 9.33 0.00 3.96
1571 1781 2.438583 CTCGTTCGTGAGTAATCCGTC 58.561 52.381 2.02 0.00 0.00 4.79
1582 1792 5.908499 GTGAGTAATCCGTCGTCTTATTCTC 59.092 44.000 0.00 0.00 0.00 2.87
1624 1852 1.184970 TGAGTGGGTCGAGACATGCA 61.185 55.000 5.55 0.00 0.00 3.96
1649 1880 0.524862 GAACTTGCAGGTCAGCATGG 59.475 55.000 0.32 0.00 45.19 3.66
1682 1913 4.373116 GCGCCCTGTCCTCGTCAA 62.373 66.667 0.00 0.00 0.00 3.18
1711 1942 7.330208 GCGTACTCTACTTCATGTTTTTCCTTA 59.670 37.037 0.00 0.00 0.00 2.69
1715 1946 7.661847 ACTCTACTTCATGTTTTTCCTTAGTGG 59.338 37.037 0.00 0.00 37.10 4.00
1719 1950 6.605594 ACTTCATGTTTTTCCTTAGTGGTGAA 59.394 34.615 0.00 0.00 37.07 3.18
1747 1978 0.898320 AGCCATTCTGTGCTACGACT 59.102 50.000 0.00 0.00 35.69 4.18
1760 1991 0.246635 TACGACTTGGGCTCTCAAGC 59.753 55.000 9.28 0.00 45.77 4.01
1810 2041 1.681793 GCTCTAACGGCCTATCACTGA 59.318 52.381 0.00 0.00 0.00 3.41
1823 2054 1.214062 CACTGAGTGACGGCTCCTC 59.786 63.158 6.79 0.00 35.23 3.71
1833 2064 2.163509 GACGGCTCCTCTATGCTCATA 58.836 52.381 0.00 0.00 0.00 2.15
1852 2083 2.706339 AGAGAATGTGGATGGCAGTC 57.294 50.000 0.00 0.00 0.00 3.51
1857 2088 1.210204 ATGTGGATGGCAGTCTGGGT 61.210 55.000 1.14 0.00 0.00 4.51
1864 2095 0.469705 TGGCAGTCTGGGTTTTGCAT 60.470 50.000 1.14 0.00 38.27 3.96
1914 2145 2.095718 GTCAAGGCAAATGAGTTCCGTC 60.096 50.000 0.00 0.00 0.00 4.79
1931 2162 1.144716 TCGGAGCTGCATCATGGAC 59.855 57.895 5.91 0.00 0.00 4.02
1941 2172 4.700700 CTGCATCATGGACTCAACATAGA 58.299 43.478 0.00 0.00 0.00 1.98
1958 2189 5.380900 ACATAGAGTCATCGATCTCAAGGA 58.619 41.667 14.54 0.00 33.63 3.36
1987 2218 1.818674 CCATTCAAAACCCCGAGGAAG 59.181 52.381 0.00 0.00 36.73 3.46
2040 2271 2.811431 GGACATCATTTTCGTGACCACA 59.189 45.455 0.85 0.00 0.00 4.17
2089 2320 6.267699 TCTCAACACACTAAGATGGAAGAAGA 59.732 38.462 0.00 0.00 0.00 2.87
2142 2373 6.588756 TGATTCCGTACATGAGTTTCTACAAC 59.411 38.462 0.00 0.00 0.00 3.32
2147 2378 3.399330 ACATGAGTTTCTACAACCCACG 58.601 45.455 0.00 0.00 0.00 4.94
2189 2420 7.950124 TCTTTCTTTTGTGATTAGGGGAATCTT 59.050 33.333 0.00 0.00 43.90 2.40
2190 2421 9.243105 CTTTCTTTTGTGATTAGGGGAATCTTA 57.757 33.333 0.00 0.00 43.90 2.10
2227 2458 5.455056 AGGTATATCACTTAGTGGAAGCG 57.545 43.478 12.79 0.00 38.92 4.68
2232 2463 1.229400 ACTTAGTGGAAGCGGGGGA 60.229 57.895 0.00 0.00 38.92 4.81
2237 2468 0.996583 AGTGGAAGCGGGGGAAAATA 59.003 50.000 0.00 0.00 0.00 1.40
2238 2469 1.569072 AGTGGAAGCGGGGGAAAATAT 59.431 47.619 0.00 0.00 0.00 1.28
2307 2538 9.534565 TTTGTTTAGAGAGATAGATATGTGTGC 57.465 33.333 0.00 0.00 0.00 4.57
2308 2539 8.470657 TGTTTAGAGAGATAGATATGTGTGCT 57.529 34.615 0.00 0.00 0.00 4.40
2309 2540 8.572185 TGTTTAGAGAGATAGATATGTGTGCTC 58.428 37.037 0.00 0.00 0.00 4.26
2310 2541 8.572185 GTTTAGAGAGATAGATATGTGTGCTCA 58.428 37.037 0.00 0.00 0.00 4.26
2311 2542 8.697507 TTAGAGAGATAGATATGTGTGCTCAA 57.302 34.615 0.00 0.00 0.00 3.02
2312 2543 7.218228 AGAGAGATAGATATGTGTGCTCAAG 57.782 40.000 0.00 0.00 0.00 3.02
2313 2544 5.782047 AGAGATAGATATGTGTGCTCAAGC 58.218 41.667 0.00 0.00 42.50 4.01
2314 2545 4.892433 AGATAGATATGTGTGCTCAAGCC 58.108 43.478 0.00 0.00 41.18 4.35
2315 2546 4.346127 AGATAGATATGTGTGCTCAAGCCA 59.654 41.667 0.00 0.00 41.18 4.75
2316 2547 3.354948 AGATATGTGTGCTCAAGCCAA 57.645 42.857 0.00 0.00 41.18 4.52
2317 2548 3.012518 AGATATGTGTGCTCAAGCCAAC 58.987 45.455 0.00 0.00 41.18 3.77
2318 2549 2.566833 TATGTGTGCTCAAGCCAACT 57.433 45.000 0.00 0.00 41.18 3.16
2319 2550 1.696063 ATGTGTGCTCAAGCCAACTT 58.304 45.000 0.00 0.00 41.18 2.66
2320 2551 1.024271 TGTGTGCTCAAGCCAACTTC 58.976 50.000 0.00 0.00 41.18 3.01
2321 2552 1.312815 GTGTGCTCAAGCCAACTTCT 58.687 50.000 0.00 0.00 41.18 2.85
2322 2553 1.678101 GTGTGCTCAAGCCAACTTCTT 59.322 47.619 0.00 0.00 41.18 2.52
2323 2554 2.099756 GTGTGCTCAAGCCAACTTCTTT 59.900 45.455 0.00 0.00 41.18 2.52
2324 2555 2.760092 TGTGCTCAAGCCAACTTCTTTT 59.240 40.909 0.00 0.00 41.18 2.27
2325 2556 3.195396 TGTGCTCAAGCCAACTTCTTTTT 59.805 39.130 0.00 0.00 41.18 1.94
2480 2743 1.228552 GCAGAAAAGGTGAGCCCCA 60.229 57.895 0.00 0.00 34.57 4.96
2498 2761 2.882761 CCCAGTGATGCGATTCATTGAT 59.117 45.455 10.69 0.00 35.91 2.57
2692 2955 4.974645 TTCCTGTACTTGAAGACATGGT 57.025 40.909 0.00 0.00 0.00 3.55
2725 2988 9.658799 TTTGTTTGGAAAACATTGAAGTTCATA 57.341 25.926 6.36 0.00 0.00 2.15
2884 3148 0.113190 CAGCCCTGGGTTTTCCTCTT 59.887 55.000 15.56 0.00 40.46 2.85
3008 3273 0.894835 TCGTACCATTGCTGAGCAGA 59.105 50.000 7.39 0.00 40.61 4.26
3029 3294 9.532494 AGCAGATGATGAAAGTATATCTAGAGT 57.468 33.333 0.00 0.00 0.00 3.24
3228 3493 7.255730 GCATGGAAACTGAATCTTTAGCCATAT 60.256 37.037 0.00 0.00 32.73 1.78
3235 3500 8.159344 ACTGAATCTTTAGCCATATGTTTAGC 57.841 34.615 1.24 0.00 0.00 3.09
3239 3504 6.844696 TCTTTAGCCATATGTTTAGCGAAG 57.155 37.500 1.24 7.86 0.00 3.79
3284 3549 7.063934 TGTCTGCTTGATGATCTCATATTCT 57.936 36.000 0.00 0.00 36.57 2.40
3288 3557 9.032624 TCTGCTTGATGATCTCATATTCTCATA 57.967 33.333 0.00 0.00 36.57 2.15
3414 3683 9.295825 GTGGGATGGAAATATTCATATGTTACA 57.704 33.333 1.90 0.00 0.00 2.41
3477 3746 0.518636 GCAGCAAGATCAACTGCGAA 59.481 50.000 15.85 0.00 46.38 4.70
3574 3843 4.746729 TCAACAACATGATTATGGCAAGC 58.253 39.130 0.00 0.00 38.66 4.01
3575 3844 4.463539 TCAACAACATGATTATGGCAAGCT 59.536 37.500 0.00 0.00 38.66 3.74
3576 3845 4.380841 ACAACATGATTATGGCAAGCTG 57.619 40.909 0.00 0.00 38.66 4.24
3578 3847 4.142315 ACAACATGATTATGGCAAGCTGTC 60.142 41.667 0.00 0.00 38.66 3.51
3580 3849 4.275810 ACATGATTATGGCAAGCTGTCTT 58.724 39.130 0.00 0.00 38.66 3.01
3581 3850 4.097437 ACATGATTATGGCAAGCTGTCTTG 59.903 41.667 0.00 7.25 43.19 3.02
3612 3882 5.163457 GCTCTCCTCTTAATGCACTAGTTCT 60.163 44.000 0.00 0.00 0.00 3.01
3667 3937 9.897744 TTGAACATAATTTTGCTAGAGACTTTG 57.102 29.630 0.00 0.00 0.00 2.77
3669 3939 8.635765 AACATAATTTTGCTAGAGACTTTGGA 57.364 30.769 0.00 0.00 0.00 3.53
3715 3986 3.304559 GCATGCTGTACTAGTTCACTTCG 59.695 47.826 11.37 0.00 0.00 3.79
3758 4031 2.441959 TTGCCCAGGCTGAGCAAT 59.558 55.556 29.34 0.00 41.35 3.56
3791 4064 7.171508 CACAAGCACTTCAAAGTCTTAGATGTA 59.828 37.037 0.00 0.00 37.08 2.29
3824 4097 5.663456 TGAATTTGCAATAAATGGCTCCTC 58.337 37.500 0.00 0.00 0.00 3.71
3825 4098 4.677673 ATTTGCAATAAATGGCTCCTCC 57.322 40.909 0.00 0.00 0.00 4.30
3826 4099 3.386932 TTGCAATAAATGGCTCCTCCT 57.613 42.857 0.00 0.00 35.26 3.69
3914 4187 3.009723 CACATCCACGTAATTGGCTCTT 58.990 45.455 0.00 0.00 36.48 2.85
4126 4403 3.495434 TTGACCTTGTACGAACCCAAT 57.505 42.857 0.00 0.00 0.00 3.16
4148 4426 2.335681 AACCCATAAAAAGGTGGGGG 57.664 50.000 14.43 1.78 45.56 5.40
4177 4455 8.579850 AGCTTAGATTTTGACAATTGTCCATA 57.420 30.769 30.66 18.21 44.15 2.74
4313 4595 8.905660 TGATTTTTGGACAACATCAAATGAAT 57.094 26.923 4.43 0.00 33.58 2.57
4349 4631 2.004017 TCATACCGCCACGACAAAATC 58.996 47.619 0.00 0.00 0.00 2.17
4350 4632 1.063469 CATACCGCCACGACAAAATCC 59.937 52.381 0.00 0.00 0.00 3.01
4370 4652 5.943349 TCCAAAAAGGGATCGTGATACTA 57.057 39.130 0.00 0.00 38.24 1.82
4408 4691 7.039223 ACTCTCTCATTCTTTGGCAAATCAAAT 60.039 33.333 13.89 10.65 36.24 2.32
4436 4719 0.951558 CTTGCCGCCTGTAAAACAGT 59.048 50.000 6.33 0.00 44.50 3.55
4454 4737 3.058708 ACAGTGTGCATTCAGTTGAATCG 60.059 43.478 4.43 3.06 42.41 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.311871 CACTGATGCTGTATGAAAGCCTC 59.688 47.826 0.00 0.00 40.06 4.70
1 2 3.054875 TCACTGATGCTGTATGAAAGCCT 60.055 43.478 0.00 0.00 40.06 4.58
2 3 3.273434 TCACTGATGCTGTATGAAAGCC 58.727 45.455 0.00 0.00 40.06 4.35
3 4 4.633126 TCTTCACTGATGCTGTATGAAAGC 59.367 41.667 0.00 0.00 41.22 3.51
6 7 9.866798 GATATATCTTCACTGATGCTGTATGAA 57.133 33.333 5.42 0.00 0.00 2.57
7 8 9.028284 TGATATATCTTCACTGATGCTGTATGA 57.972 33.333 13.79 0.00 0.00 2.15
8 9 9.649167 TTGATATATCTTCACTGATGCTGTATG 57.351 33.333 13.79 0.00 0.00 2.39
10 11 9.866798 GATTGATATATCTTCACTGATGCTGTA 57.133 33.333 13.79 0.00 0.00 2.74
11 12 8.373220 TGATTGATATATCTTCACTGATGCTGT 58.627 33.333 13.79 0.00 0.00 4.40
12 13 8.773404 TGATTGATATATCTTCACTGATGCTG 57.227 34.615 13.79 0.00 0.00 4.41
13 14 9.602568 GATGATTGATATATCTTCACTGATGCT 57.397 33.333 13.79 1.48 32.10 3.79
14 15 9.379791 TGATGATTGATATATCTTCACTGATGC 57.620 33.333 13.79 5.00 35.20 3.91
17 18 9.924650 CACTGATGATTGATATATCTTCACTGA 57.075 33.333 13.79 4.68 35.20 3.41
18 19 9.924650 TCACTGATGATTGATATATCTTCACTG 57.075 33.333 13.79 14.23 35.20 3.66
28 29 9.671279 TTGTACAACTTCACTGATGATTGATAT 57.329 29.630 3.59 0.00 33.85 1.63
29 30 9.500785 TTTGTACAACTTCACTGATGATTGATA 57.499 29.630 8.07 0.00 33.85 2.15
30 31 7.984422 TTGTACAACTTCACTGATGATTGAT 57.016 32.000 3.59 0.00 33.85 2.57
31 32 7.800155 TTTGTACAACTTCACTGATGATTGA 57.200 32.000 8.07 0.00 33.85 2.57
36 37 9.897744 ACAATAATTTGTACAACTTCACTGATG 57.102 29.630 13.80 8.37 44.22 3.07
59 60 4.116961 CCGTTTCAGAGTCAACACTACAA 58.883 43.478 0.00 0.00 30.63 2.41
61 62 3.714391 ACCGTTTCAGAGTCAACACTAC 58.286 45.455 0.00 0.00 30.63 2.73
74 75 4.903054 TCTACTGTCTCTCTACCGTTTCA 58.097 43.478 0.00 0.00 0.00 2.69
75 76 4.937015 ACTCTACTGTCTCTCTACCGTTTC 59.063 45.833 0.00 0.00 0.00 2.78
83 84 4.643463 TCGACAAACTCTACTGTCTCTCT 58.357 43.478 1.21 0.00 39.87 3.10
91 92 4.201970 GCTAGAGCATCGACAAACTCTACT 60.202 45.833 10.04 0.00 42.67 2.57
113 114 0.799534 GCAGCGTGTTGGAATCATGC 60.800 55.000 0.00 0.00 44.95 4.06
127 128 5.478233 TGTACATTATTACTTTGGCAGCG 57.522 39.130 0.00 0.00 0.00 5.18
131 132 9.072294 GTTTGACATGTACATTATTACTTTGGC 57.928 33.333 5.37 0.00 0.00 4.52
288 289 4.886579 TGGACGTTTTAGGGTTTAGAGAC 58.113 43.478 0.00 0.00 0.00 3.36
362 394 3.005472 GCTGGAGCGTTATATGTACCTGA 59.995 47.826 0.00 0.00 0.00 3.86
390 422 7.722949 TTCTTGGCCTTTCATCATAAAATCT 57.277 32.000 3.32 0.00 0.00 2.40
521 554 8.593679 TCAACTTCAACATTCAGTCTCCTATAA 58.406 33.333 0.00 0.00 0.00 0.98
582 615 5.119434 TCGAAAAACCAAACTGAAGTTTTGC 59.881 36.000 5.70 0.00 45.07 3.68
686 719 7.685481 TCCTCAACATCCTACAAAACAATAGA 58.315 34.615 0.00 0.00 0.00 1.98
687 720 7.921786 TCCTCAACATCCTACAAAACAATAG 57.078 36.000 0.00 0.00 0.00 1.73
688 721 8.877864 AATCCTCAACATCCTACAAAACAATA 57.122 30.769 0.00 0.00 0.00 1.90
689 722 7.781324 AATCCTCAACATCCTACAAAACAAT 57.219 32.000 0.00 0.00 0.00 2.71
690 723 7.286546 TCAAATCCTCAACATCCTACAAAACAA 59.713 33.333 0.00 0.00 0.00 2.83
692 725 7.214467 TCAAATCCTCAACATCCTACAAAAC 57.786 36.000 0.00 0.00 0.00 2.43
720 755 8.526147 AGGCATGTTAATTGGCTTATATGAATC 58.474 33.333 10.47 0.00 46.70 2.52
721 756 8.308931 CAGGCATGTTAATTGGCTTATATGAAT 58.691 33.333 12.81 0.00 46.70 2.57
796 961 6.824305 TTTCTTCTCCACATGAGGATTTTC 57.176 37.500 12.62 0.00 41.76 2.29
810 975 2.218603 TGTTGCTCGGTTTTCTTCTCC 58.781 47.619 0.00 0.00 0.00 3.71
822 992 2.357881 TGCTCCTGCTGTTGCTCG 60.358 61.111 6.61 0.00 40.48 5.03
863 1033 4.101448 AGCATCCGACAGGTGGGC 62.101 66.667 0.00 0.00 39.05 5.36
913 1083 2.551504 GGGAGAAAAGGTTTAGCGGACA 60.552 50.000 0.00 0.00 0.00 4.02
1156 1351 1.629861 TGCATCTCCATGGAACTCACA 59.370 47.619 17.00 7.90 0.00 3.58
1568 1778 5.676532 ACTCCTATGAGAATAAGACGACG 57.323 43.478 1.64 0.00 41.42 5.12
1571 1781 9.186323 CACAATTACTCCTATGAGAATAAGACG 57.814 37.037 1.64 0.00 41.42 4.18
1582 1792 7.674120 TCATCCTCATCACAATTACTCCTATG 58.326 38.462 0.00 0.00 0.00 2.23
1624 1852 2.555757 GCTGACCTGCAAGTTCAAGATT 59.444 45.455 0.00 0.00 0.00 2.40
1661 1892 2.292794 GACGAGGACAGGGCGCATTA 62.293 60.000 10.83 0.00 0.00 1.90
1681 1912 2.490903 ACATGAAGTAGAGTACGCCGTT 59.509 45.455 0.00 0.00 0.00 4.44
1682 1913 2.089980 ACATGAAGTAGAGTACGCCGT 58.910 47.619 0.00 0.00 0.00 5.68
1711 1942 2.840038 TGGCTATGTCATCTTCACCACT 59.160 45.455 0.00 0.00 0.00 4.00
1715 1946 5.007430 CACAGAATGGCTATGTCATCTTCAC 59.993 44.000 0.00 0.00 43.62 3.18
1719 1950 3.136077 AGCACAGAATGGCTATGTCATCT 59.864 43.478 0.00 0.00 43.62 2.90
1760 1991 5.243954 TCCGGTAGATGAATCAGTGATAAGG 59.756 44.000 5.94 0.00 0.00 2.69
1810 2041 0.396417 AGCATAGAGGAGCCGTCACT 60.396 55.000 0.00 0.00 0.00 3.41
1823 2054 6.107343 CCATCCACATTCTCTATGAGCATAG 58.893 44.000 10.53 10.53 41.58 2.23
1833 2064 2.093075 CAGACTGCCATCCACATTCTCT 60.093 50.000 0.00 0.00 0.00 3.10
1914 2145 0.879400 GAGTCCATGATGCAGCTCCG 60.879 60.000 2.53 0.00 0.00 4.63
1931 2162 6.311055 TGAGATCGATGACTCTATGTTGAG 57.689 41.667 0.54 0.00 39.78 3.02
1941 2172 4.709397 AGACTTTCCTTGAGATCGATGACT 59.291 41.667 0.54 0.00 0.00 3.41
1958 2189 3.239449 GGGTTTTGAATGGGGAGACTTT 58.761 45.455 0.00 0.00 0.00 2.66
1987 2218 2.122768 AGATCCCATCAAGTCAGGTCC 58.877 52.381 0.00 0.00 0.00 4.46
2061 2292 6.875726 TCTTCCATCTTAGTGTGTTGAGATTG 59.124 38.462 0.00 0.00 0.00 2.67
2070 2301 7.730084 TCCATATCTTCTTCCATCTTAGTGTG 58.270 38.462 0.00 0.00 0.00 3.82
2089 2320 8.016054 AGTAGGGAATTCTTCTCTCTTCCATAT 58.984 37.037 5.23 0.00 40.40 1.78
2114 2345 5.655488 AGAAACTCATGTACGGAATCAGAG 58.345 41.667 0.00 0.00 0.00 3.35
2118 2349 6.035758 GGTTGTAGAAACTCATGTACGGAATC 59.964 42.308 0.00 0.00 0.00 2.52
2147 2378 0.315568 AAGACACAGAGACGCACCTC 59.684 55.000 0.00 0.00 0.00 3.85
2160 2391 5.768164 TCCCCTAATCACAAAAGAAAGACAC 59.232 40.000 0.00 0.00 0.00 3.67
2203 2434 6.153000 CCGCTTCCACTAAGTGATATACCTAT 59.847 42.308 0.00 0.00 46.72 2.57
2323 2554 3.641648 CTTGAGCAATTCCAGCGAAAAA 58.358 40.909 0.00 0.00 37.01 1.94
2324 2555 2.607771 GCTTGAGCAATTCCAGCGAAAA 60.608 45.455 0.00 0.00 41.59 2.29
2325 2556 1.068333 GCTTGAGCAATTCCAGCGAAA 60.068 47.619 0.00 0.00 41.59 3.46
2326 2557 0.523072 GCTTGAGCAATTCCAGCGAA 59.477 50.000 0.00 0.00 41.59 4.70
2327 2558 2.174334 GCTTGAGCAATTCCAGCGA 58.826 52.632 0.00 0.00 41.59 4.93
2328 2559 4.779819 GCTTGAGCAATTCCAGCG 57.220 55.556 0.00 0.00 41.59 5.18
2480 2743 5.239963 TGCATTATCAATGAATCGCATCACT 59.760 36.000 3.11 0.00 41.46 3.41
2725 2988 2.242043 CCAATGGAGTGAGTTTTGCCT 58.758 47.619 0.00 0.00 0.00 4.75
2821 3085 2.881513 TGTACGTGCACATGGTTCAATT 59.118 40.909 18.64 0.00 0.00 2.32
2822 3086 2.499197 TGTACGTGCACATGGTTCAAT 58.501 42.857 18.64 0.00 0.00 2.57
2884 3148 6.900186 TCCCCCTCTGCAATCAATTTTTAATA 59.100 34.615 0.00 0.00 0.00 0.98
2938 3203 8.292011 CTGGAAGAGCAAACTGTGGAGTTTTT 62.292 42.308 0.00 0.00 42.76 1.94
2942 3207 1.490490 TGGAAGAGCAAACTGTGGAGT 59.510 47.619 0.00 0.00 0.00 3.85
2943 3208 2.149578 CTGGAAGAGCAAACTGTGGAG 58.850 52.381 0.00 0.00 34.07 3.86
2959 3224 5.698741 TTAAAGAATGGATCAGAGCTGGA 57.301 39.130 0.00 0.00 0.00 3.86
2994 3259 2.572290 TCATCATCTGCTCAGCAATGG 58.428 47.619 16.84 3.99 38.41 3.16
3029 3294 7.286546 TCAATTCTTGGATGACAAAACCACTAA 59.713 33.333 0.00 0.00 38.91 2.24
3066 3331 0.750850 GCAGGCCATCATGCAGAAAT 59.249 50.000 5.01 0.00 42.11 2.17
3228 3493 5.047847 GCATATCCTGTACTTCGCTAAACA 58.952 41.667 0.00 0.00 0.00 2.83
3235 3500 6.040247 TGTAGTTTGCATATCCTGTACTTCG 58.960 40.000 0.00 0.00 0.00 3.79
3239 3504 6.986817 AGACATGTAGTTTGCATATCCTGTAC 59.013 38.462 0.00 0.00 0.00 2.90
3284 3549 6.094719 GCTGAAGCAATGAAAACATGTATGA 58.905 36.000 0.00 0.00 41.59 2.15
3316 3585 3.630312 TCAACAAGTACCTGGCAGTTTTC 59.370 43.478 14.43 1.15 0.00 2.29
3324 3593 6.677913 CCAAAAGTATTCAACAAGTACCTGG 58.322 40.000 0.00 0.00 0.00 4.45
3488 3757 4.659111 TGGCAATTGATCATCAACATCC 57.341 40.909 10.34 4.60 39.45 3.51
3504 3773 1.340088 ACCTGCAATGTTCATGGCAA 58.660 45.000 14.57 1.57 35.59 4.52
3540 3809 2.783135 TGTTGTTGATTCAGAGAGGCC 58.217 47.619 0.00 0.00 0.00 5.19
3545 3814 6.916387 GCCATAATCATGTTGTTGATTCAGAG 59.084 38.462 3.14 0.00 43.50 3.35
3574 3843 1.672441 GGAGAGCTGACAGCAAGACAG 60.672 57.143 28.43 4.73 45.56 3.51
3575 3844 0.319728 GGAGAGCTGACAGCAAGACA 59.680 55.000 28.43 0.00 45.56 3.41
3576 3845 0.607620 AGGAGAGCTGACAGCAAGAC 59.392 55.000 28.43 15.60 45.56 3.01
3578 3847 0.896923 AGAGGAGAGCTGACAGCAAG 59.103 55.000 28.43 0.00 45.56 4.01
3580 3849 2.222227 TAAGAGGAGAGCTGACAGCA 57.778 50.000 28.43 2.08 45.56 4.41
3581 3850 3.456280 CATTAAGAGGAGAGCTGACAGC 58.544 50.000 20.12 20.12 42.84 4.40
3582 3851 3.118847 TGCATTAAGAGGAGAGCTGACAG 60.119 47.826 0.00 0.00 0.00 3.51
3583 3852 2.833943 TGCATTAAGAGGAGAGCTGACA 59.166 45.455 0.00 0.00 0.00 3.58
3584 3853 3.118811 AGTGCATTAAGAGGAGAGCTGAC 60.119 47.826 0.00 0.00 0.00 3.51
3585 3854 3.102972 AGTGCATTAAGAGGAGAGCTGA 58.897 45.455 0.00 0.00 0.00 4.26
3612 3882 5.412594 GCTAATCACAATGGACAACTGAAGA 59.587 40.000 0.00 0.00 0.00 2.87
3667 3937 3.952323 GGGGTTAATAGACAGCCTTTTCC 59.048 47.826 0.00 0.00 0.00 3.13
3669 3939 4.540502 AGAGGGGTTAATAGACAGCCTTTT 59.459 41.667 0.00 0.00 0.00 2.27
3673 3943 2.485657 GCAGAGGGGTTAATAGACAGCC 60.486 54.545 0.00 0.00 0.00 4.85
3715 3986 1.525535 CACTGCATAGCCCTGAGCC 60.526 63.158 0.00 0.00 45.47 4.70
3842 4115 5.124936 CCTTGCAATCTCTGATCAAACATGA 59.875 40.000 0.00 0.00 0.00 3.07
3843 4116 5.340803 CCTTGCAATCTCTGATCAAACATG 58.659 41.667 0.00 0.00 0.00 3.21
3844 4117 4.401519 CCCTTGCAATCTCTGATCAAACAT 59.598 41.667 0.00 0.00 0.00 2.71
3845 4118 3.760151 CCCTTGCAATCTCTGATCAAACA 59.240 43.478 0.00 0.00 0.00 2.83
3851 4124 3.521126 AGTGTACCCTTGCAATCTCTGAT 59.479 43.478 0.00 0.00 0.00 2.90
3860 4133 1.202758 CCACTTCAGTGTACCCTTGCA 60.203 52.381 6.22 0.00 44.21 4.08
3881 4154 3.057456 ACGTGGATGTGAGTGACTCTTAC 60.057 47.826 14.42 5.16 33.92 2.34
3914 4187 7.224297 ACTGAAGTTACAGATTTTGAGGCTTA 58.776 34.615 0.00 0.00 40.63 3.09
4115 4392 7.771927 TTTTATGGGTTTAATTGGGTTCGTA 57.228 32.000 0.00 0.00 0.00 3.43
4117 4394 6.592220 CCTTTTTATGGGTTTAATTGGGTTCG 59.408 38.462 0.00 0.00 0.00 3.95
4126 4403 4.168883 CCCCCACCTTTTTATGGGTTTAA 58.831 43.478 8.46 0.00 39.89 1.52
4148 4426 5.928264 ACAATTGTCAAAATCTAAGCTTGGC 59.072 36.000 9.86 0.00 0.00 4.52
4313 4595 5.561145 GCGGTATGACAACAACATTTGTACA 60.561 40.000 0.00 0.00 44.59 2.90
4349 4631 6.598064 ACTTTAGTATCACGATCCCTTTTTGG 59.402 38.462 0.00 0.00 0.00 3.28
4350 4632 7.611213 ACTTTAGTATCACGATCCCTTTTTG 57.389 36.000 0.00 0.00 0.00 2.44
4370 4652 9.956640 AAAGAATGAGAGAGTCATGATAACTTT 57.043 29.630 0.00 0.00 45.89 2.66
4436 4719 2.226200 CACCGATTCAACTGAATGCACA 59.774 45.455 9.63 0.00 44.14 4.57
4454 4737 4.782019 TTTACATCCAACAATCTGCACC 57.218 40.909 0.00 0.00 0.00 5.01


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

AutoCloner maintained by Alex Coulton.