Multiple sequence alignment - TraesCS7D01G253800

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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 TraesCS7D01G253800 chr7D 100.000 4209 0 0 1001 5209 230494807 230490599 0.000000e+00 7773.0
1 TraesCS7D01G253800 chr7D 100.000 605 0 0 1 605 230495807 230495203 0.000000e+00 1118.0
2 TraesCS7D01G253800 chr7D 79.775 178 28 6 2059 2228 151270696 151270873 7.080000e-24 122.0
3 TraesCS7D01G253800 chr7A 91.867 2459 98 33 1830 4256 243366090 243363702 0.000000e+00 3339.0
4 TraesCS7D01G253800 chr7A 89.235 771 54 12 1018 1787 243366838 243366096 0.000000e+00 937.0
5 TraesCS7D01G253800 chr7A 92.308 455 18 5 4255 4708 243363588 243363150 9.520000e-177 630.0
6 TraesCS7D01G253800 chr7A 78.309 816 121 41 2682 3457 150982904 150983703 4.720000e-130 475.0
7 TraesCS7D01G253800 chr7A 93.117 247 12 4 4965 5209 243362586 243362343 1.780000e-94 357.0
8 TraesCS7D01G253800 chr7A 81.863 408 44 15 1 402 243367514 243367131 3.030000e-82 316.0
9 TraesCS7D01G253800 chr7A 84.818 303 23 2 4665 4967 243363151 243362872 3.070000e-72 283.0
10 TraesCS7D01G253800 chr7A 92.701 137 2 4 477 605 243367072 243366936 1.910000e-44 191.0
11 TraesCS7D01G253800 chr7A 77.559 254 48 9 4711 4959 62482698 62482449 1.510000e-30 145.0
12 TraesCS7D01G253800 chr7A 80.000 175 28 6 2059 2228 150982072 150982244 7.080000e-24 122.0
13 TraesCS7D01G253800 chr7A 100.000 41 0 0 396 436 243367115 243367075 5.590000e-10 76.8
14 TraesCS7D01G253800 chr7B 93.710 1892 92 15 2373 4256 201499566 201497694 0.000000e+00 2809.0
15 TraesCS7D01G253800 chr7B 88.248 1404 108 22 1018 2377 201523551 201522161 0.000000e+00 1626.0
16 TraesCS7D01G253800 chr7B 78.761 791 114 40 2682 3432 113161504 113162280 1.010000e-131 481.0
17 TraesCS7D01G253800 chr7B 87.293 181 6 7 442 605 201523830 201523650 1.910000e-44 191.0
18 TraesCS7D01G253800 chr7B 89.655 145 14 1 4831 4975 201497196 201497053 3.200000e-42 183.0
19 TraesCS7D01G253800 chr7B 89.655 145 2 4 4255 4395 201497532 201497397 6.930000e-39 172.0
20 TraesCS7D01G253800 chr7B 86.364 110 13 2 2119 2228 113160739 113160846 9.160000e-23 119.0
21 TraesCS7D01G253800 chr7B 79.630 108 12 7 4719 4819 600595298 600595402 9.360000e-08 69.4
22 TraesCS7D01G253800 chr4A 80.879 455 69 15 2682 3127 725940021 725939576 4.990000e-90 342.0
23 TraesCS7D01G253800 chr3B 77.567 263 38 17 4712 4965 811503660 811503410 7.030000e-29 139.0
24 TraesCS7D01G253800 chr1A 87.500 104 11 2 4720 4822 448626810 448626708 9.160000e-23 119.0
25 TraesCS7D01G253800 chr2B 88.889 90 8 2 4710 4797 662897040 662897129 5.510000e-20 110.0
26 TraesCS7D01G253800 chr2B 79.221 154 25 4 4709 4858 555519767 555519917 3.320000e-17 100.0
27 TraesCS7D01G253800 chr3D 87.209 86 10 1 4847 4931 71762962 71763047 4.290000e-16 97.1
28 TraesCS7D01G253800 chr5D 80.000 105 20 1 4718 4821 484566464 484566360 5.590000e-10 76.8
29 TraesCS7D01G253800 chrUn 81.818 88 16 0 4719 4806 17300675 17300762 2.010000e-09 75.0
30 TraesCS7D01G253800 chr1D 81.319 91 15 2 4730 4819 438318947 438319036 7.240000e-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 TraesCS7D01G253800 chr7D 230490599 230495807 5208 True 4445.500000 7773 100.000000 1 5209 2 chr7D.!!$R1 5208
1 TraesCS7D01G253800 chr7A 243362343 243367514 5171 True 766.225000 3339 90.738625 1 5209 8 chr7A.!!$R2 5208
2 TraesCS7D01G253800 chr7A 150982072 150983703 1631 False 298.500000 475 79.154500 2059 3457 2 chr7A.!!$F1 1398
3 TraesCS7D01G253800 chr7B 201497053 201499566 2513 True 1054.666667 2809 91.006667 2373 4975 3 chr7B.!!$R1 2602
4 TraesCS7D01G253800 chr7B 201522161 201523830 1669 True 908.500000 1626 87.770500 442 2377 2 chr7B.!!$R2 1935
5 TraesCS7D01G253800 chr7B 113160739 113162280 1541 False 300.000000 481 82.562500 2119 3432 2 chr7B.!!$F2 1313

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
62 66 0.106819 GAAGGCAGCTCATCACCCAT 60.107 55.0 0.00 0.0 0.00 4.00 F
1364 1419 0.039165 CCGCTTTGCCTGAAGGTTTC 60.039 55.0 0.00 0.0 37.57 2.78 F
1466 1521 0.400213 TCGTTGGCTCCAGTGGAATT 59.600 50.0 14.17 0.0 0.00 2.17 F
2256 2349 0.044092 TATGGCAAGTCCCTCTCCCA 59.956 55.0 0.00 0.0 0.00 4.37 F
3158 3528 0.250124 TGTTGACCCCGTCACATGAC 60.250 55.0 0.00 1.7 42.60 3.06 F
3687 4072 1.607225 TAATGGAGGATGCCCCAACT 58.393 50.0 0.00 0.0 35.85 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1514 1577 0.871057 GCACCAGCTCTCAGTTTGAC 59.129 55.000 0.00 0.0 37.91 3.18 R
2170 2263 0.107831 GCCCGGATAGCACAATGGTA 59.892 55.000 0.73 0.0 34.60 3.25 R
2639 2973 0.871722 CCGTTGAATTGCGTCAAGGA 59.128 50.000 15.01 0.0 43.04 3.36 R
3671 4056 0.253160 AGTAGTTGGGGCATCCTCCA 60.253 55.000 0.00 0.0 36.20 3.86 R
4214 4602 1.008538 GCAGCAACAACGAACAGGG 60.009 57.895 0.00 0.0 0.00 4.45 R
4791 5503 1.068434 GCTTGCCAACTAAACTTGCCA 59.932 47.619 0.00 0.0 0.00 4.92 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 25 3.382832 AAGCCGTCTCCTCCGTGG 61.383 66.667 0.00 0.00 37.10 4.94
27 31 3.311110 TCTCCTCCGTGGCGCTTT 61.311 61.111 7.64 0.00 35.26 3.51
49 53 4.649190 TGAACTTTCACACCCGAAGGCA 62.649 50.000 0.00 0.00 38.35 4.75
59 63 1.817099 CCGAAGGCAGCTCATCACC 60.817 63.158 0.00 0.00 46.14 4.02
62 66 0.106819 GAAGGCAGCTCATCACCCAT 60.107 55.000 0.00 0.00 0.00 4.00
74 78 0.625316 TCACCCATAAGCTGCCACAT 59.375 50.000 0.00 0.00 0.00 3.21
75 79 1.843206 TCACCCATAAGCTGCCACATA 59.157 47.619 0.00 0.00 0.00 2.29
81 85 5.163416 ACCCATAAGCTGCCACATAAAAATC 60.163 40.000 0.00 0.00 0.00 2.17
106 111 2.125431 GCCAATGCCATGGTGTGC 60.125 61.111 14.67 5.89 42.75 4.57
111 116 1.545136 CAATGCCATGGTGTGCAACTA 59.455 47.619 14.67 0.00 41.50 2.24
117 122 2.485426 CCATGGTGTGCAACTACTTCAG 59.515 50.000 2.57 0.00 38.04 3.02
147 152 3.191371 GGCTCTGACGTCAATCCAAATTT 59.809 43.478 20.49 0.00 0.00 1.82
148 153 4.321230 GGCTCTGACGTCAATCCAAATTTT 60.321 41.667 20.49 0.00 0.00 1.82
149 154 5.222631 GCTCTGACGTCAATCCAAATTTTT 58.777 37.500 20.49 0.00 0.00 1.94
165 170 7.281999 TCCAAATTTTTCCTTAGCAAGTTTTGG 59.718 33.333 0.00 0.00 40.27 3.28
166 171 6.618287 AATTTTTCCTTAGCAAGTTTTGGC 57.382 33.333 0.00 0.00 0.00 4.52
173 178 4.159135 CCTTAGCAAGTTTTGGCATCAGAT 59.841 41.667 0.00 0.00 0.00 2.90
174 179 3.863142 AGCAAGTTTTGGCATCAGATC 57.137 42.857 0.00 0.00 0.00 2.75
176 181 2.733227 GCAAGTTTTGGCATCAGATCGG 60.733 50.000 0.00 0.00 0.00 4.18
184 189 0.465705 GCATCAGATCGGACCTGGAA 59.534 55.000 0.00 0.00 32.73 3.53
204 209 7.658525 TGGAAGGCATATGATTTTGTAATGT 57.341 32.000 6.97 0.00 0.00 2.71
205 210 8.759481 TGGAAGGCATATGATTTTGTAATGTA 57.241 30.769 6.97 0.00 0.00 2.29
206 211 8.629158 TGGAAGGCATATGATTTTGTAATGTAC 58.371 33.333 6.97 0.00 0.00 2.90
207 212 8.850156 GGAAGGCATATGATTTTGTAATGTACT 58.150 33.333 6.97 0.00 0.00 2.73
230 235 2.696125 GGGGCCAGATTCCCTCCA 60.696 66.667 4.39 0.00 43.41 3.86
233 238 0.178978 GGGCCAGATTCCCTCCAATC 60.179 60.000 4.39 0.00 40.66 2.67
242 247 5.126061 CAGATTCCCTCCAATCGTTGATTTT 59.874 40.000 0.15 0.00 37.77 1.82
265 272 1.732941 TCGTGGGGATCGTTGATTTG 58.267 50.000 0.00 0.00 0.00 2.32
266 273 1.002659 TCGTGGGGATCGTTGATTTGT 59.997 47.619 0.00 0.00 0.00 2.83
321 328 8.421249 AAATTATTTGAAATGGTGTCTGAGGA 57.579 30.769 0.00 0.00 0.00 3.71
322 329 6.817765 TTATTTGAAATGGTGTCTGAGGAC 57.182 37.500 0.00 0.00 42.42 3.85
375 382 1.335872 CGGTGAGGACAAATTTGGCAC 60.336 52.381 25.05 21.34 38.18 5.01
393 400 2.286833 GCACCAAATTGATCATGCATGC 59.713 45.455 22.25 11.82 33.27 4.06
394 401 2.869801 CACCAAATTGATCATGCATGCC 59.130 45.455 22.25 15.63 0.00 4.40
469 497 1.300971 CTGCCTTACGTGCATGCTGT 61.301 55.000 20.33 18.93 38.22 4.40
1200 1254 0.674581 TGCTCCTCGCAGGTGATTTG 60.675 55.000 8.01 0.00 45.47 2.32
1306 1361 5.238214 CCTGAAAAACTAGGCAGATAGATGC 59.762 44.000 0.00 0.00 45.74 3.91
1362 1417 1.150536 TCCGCTTTGCCTGAAGGTT 59.849 52.632 0.00 0.00 37.57 3.50
1364 1419 0.039165 CCGCTTTGCCTGAAGGTTTC 60.039 55.000 0.00 0.00 37.57 2.78
1416 1471 7.892609 TGTGTAGCTCTAGTTTTTGACTGATA 58.107 34.615 0.00 0.00 39.48 2.15
1417 1472 8.029522 TGTGTAGCTCTAGTTTTTGACTGATAG 58.970 37.037 0.00 0.00 39.48 2.08
1418 1473 8.030106 GTGTAGCTCTAGTTTTTGACTGATAGT 58.970 37.037 0.00 0.00 39.48 2.12
1419 1474 9.239551 TGTAGCTCTAGTTTTTGACTGATAGTA 57.760 33.333 0.00 0.00 39.48 1.82
1452 1507 1.195448 GGATGAGCAGTTGTGTCGTTG 59.805 52.381 0.00 0.00 0.00 4.10
1456 1511 1.160329 AGCAGTTGTGTCGTTGGCTC 61.160 55.000 0.00 0.00 0.00 4.70
1462 1517 1.961277 GTGTCGTTGGCTCCAGTGG 60.961 63.158 1.40 1.40 0.00 4.00
1466 1521 0.400213 TCGTTGGCTCCAGTGGAATT 59.600 50.000 14.17 0.00 0.00 2.17
1471 1526 1.177401 GGCTCCAGTGGAATTTCACC 58.823 55.000 14.17 4.45 38.34 4.02
1483 1546 5.627780 GTGGAATTTCACCACGTTCAAATAC 59.372 40.000 5.47 0.00 46.15 1.89
1488 1551 5.676532 TTCACCACGTTCAAATACGATTT 57.323 34.783 2.93 0.00 43.99 2.17
1489 1552 5.676532 TCACCACGTTCAAATACGATTTT 57.323 34.783 2.93 0.00 43.99 1.82
1490 1553 6.782298 TCACCACGTTCAAATACGATTTTA 57.218 33.333 2.93 0.00 43.99 1.52
1514 1577 1.856629 AATTGAGTCCATGCCTTGGG 58.143 50.000 3.18 0.00 46.45 4.12
1597 1660 6.316890 GCCGTTTCCTGTTTAATTATACTGGA 59.683 38.462 22.23 22.23 39.63 3.86
1728 1791 3.196613 AACGGAAGCAGAGACGTTC 57.803 52.632 0.00 0.00 45.15 3.95
1747 1810 6.913170 ACGTTCAAATTGTCAGCTGATTTAT 58.087 32.000 21.47 10.74 0.00 1.40
1794 1857 2.969950 AGGTGTAGCAAGTTAGTGGTGA 59.030 45.455 0.00 0.00 0.00 4.02
1799 1862 5.296035 GTGTAGCAAGTTAGTGGTGAAGTTT 59.704 40.000 0.00 0.00 0.00 2.66
1810 1873 9.575783 GTTAGTGGTGAAGTTTTGTTGATTTTA 57.424 29.630 0.00 0.00 0.00 1.52
1813 1876 7.926018 AGTGGTGAAGTTTTGTTGATTTTATCC 59.074 33.333 0.00 0.00 0.00 2.59
1815 1878 6.128929 GGTGAAGTTTTGTTGATTTTATCCGC 60.129 38.462 0.00 0.00 0.00 5.54
1821 1884 9.482627 AGTTTTGTTGATTTTATCCGCATTTAA 57.517 25.926 0.00 0.00 0.00 1.52
1840 1903 9.033481 GCATTTAATATTTGAAAGTGCATGCTA 57.967 29.630 20.33 2.15 0.00 3.49
1913 1976 2.008329 GCTTCTGGCAGAGTGAGAATG 58.992 52.381 17.91 0.00 41.35 2.67
1915 1978 3.682155 GCTTCTGGCAGAGTGAGAATGAT 60.682 47.826 17.91 0.00 41.35 2.45
2044 2108 5.460646 ACATTGTTGTATTGCTGTACTTGC 58.539 37.500 0.00 0.00 33.16 4.01
2045 2109 4.497473 TTGTTGTATTGCTGTACTTGCC 57.503 40.909 8.51 0.00 0.00 4.52
2051 2138 4.935205 TGTATTGCTGTACTTGCCTACTTG 59.065 41.667 8.51 0.00 0.00 3.16
2129 2221 5.349061 TTGATGAGCAGTGTATGTCTGAT 57.651 39.130 0.00 0.00 35.20 2.90
2170 2263 8.733458 TCTTGTCTGAAATCATCGAAATCAAAT 58.267 29.630 0.00 0.00 0.00 2.32
2256 2349 0.044092 TATGGCAAGTCCCTCTCCCA 59.956 55.000 0.00 0.00 0.00 4.37
2258 2351 2.671682 GCAAGTCCCTCTCCCACC 59.328 66.667 0.00 0.00 0.00 4.61
2260 2353 1.904990 GCAAGTCCCTCTCCCACCTC 61.905 65.000 0.00 0.00 0.00 3.85
2298 2434 4.160439 TCACATTCTAGTGGCCAGAGTAAG 59.840 45.833 5.11 0.00 39.93 2.34
2339 2487 6.017192 GGTTTGCTAATTTGATTGCCAGTTTT 60.017 34.615 0.00 0.00 0.00 2.43
2369 2517 6.205464 TCTCTCTTCATTGCCAAGTTTTAGTG 59.795 38.462 0.00 0.00 0.00 2.74
2405 2725 4.422840 TGATATTTGTTTGCAATCTGCCG 58.577 39.130 0.00 0.00 44.23 5.69
2414 2734 3.485947 TGCAATCTGCCGTTGTTTATC 57.514 42.857 0.00 0.00 44.23 1.75
2475 2806 8.141268 AGCTTAACTTCTACTCTGATTGCTATC 58.859 37.037 0.76 0.76 0.00 2.08
2479 2810 4.733972 TCTACTCTGATTGCTATCGTCG 57.266 45.455 3.70 0.00 33.23 5.12
2653 2987 7.171508 TCACTCATATTATCCTTGACGCAATTC 59.828 37.037 0.00 0.00 0.00 2.17
2716 3053 2.526432 TCCTCTTCCTGTTAGCTTCGT 58.474 47.619 0.00 0.00 0.00 3.85
2722 3059 1.207089 TCCTGTTAGCTTCGTGATGGG 59.793 52.381 0.00 0.00 0.00 4.00
2829 3167 7.654923 GCTGTTTTCTTGGAGATGAATCTTTTT 59.345 33.333 0.00 0.00 37.25 1.94
2878 3224 7.769044 TCAAAGGCTACCATTCTTTATACAGAC 59.231 37.037 0.00 0.00 0.00 3.51
2948 3294 2.360165 CACTCTGCAGAAAGGCAAAGTT 59.640 45.455 18.85 0.00 42.14 2.66
3149 3519 1.263356 TTCTACTCCTGTTGACCCCG 58.737 55.000 0.00 0.00 0.00 5.73
3158 3528 0.250124 TGTTGACCCCGTCACATGAC 60.250 55.000 0.00 1.70 42.60 3.06
3248 3619 7.549134 TCTGGTGCAGTTAGTAACTTGATAATG 59.451 37.037 13.00 2.66 40.46 1.90
3266 3637 8.575565 TGATAATGTTCTTACAGTTATCTCGC 57.424 34.615 0.24 0.00 37.77 5.03
3501 3883 9.277783 GCTGGAATCTACAGTAAATTATGTGAT 57.722 33.333 0.00 1.60 38.22 3.06
3687 4072 1.607225 TAATGGAGGATGCCCCAACT 58.393 50.000 0.00 0.00 35.85 3.16
3717 4102 5.652518 ACAGACTAGGTTAAAGCGATTCTC 58.347 41.667 0.00 0.00 0.00 2.87
3730 4115 6.428385 AAGCGATTCTCAAATTCTACAAGG 57.572 37.500 0.00 0.00 0.00 3.61
3737 4122 3.826157 CTCAAATTCTACAAGGCCCAACA 59.174 43.478 0.00 0.00 0.00 3.33
3749 4134 6.541907 ACAAGGCCCAACAATGATTATTTTT 58.458 32.000 0.00 0.00 0.00 1.94
3816 4201 4.001652 CTGCTGACATCACTGATGAAGTT 58.998 43.478 23.30 3.05 42.09 2.66
3958 4343 3.190874 GTCAGGGCTTAGATTTGTCTCG 58.809 50.000 0.00 0.00 0.00 4.04
4006 4393 3.911661 GCAGAATTGCTGTCTGAGTTT 57.088 42.857 13.79 0.00 46.95 2.66
4079 4466 6.106003 TCTGTAGATGTGTAACGATTTGCAT 58.894 36.000 0.00 0.00 42.39 3.96
4214 4602 9.601217 AACAGTTGGTTATTCTGTCTATGATAC 57.399 33.333 0.00 0.00 40.81 2.24
4258 4809 5.839621 TGCCGTTAACCATTCTATCTAGAC 58.160 41.667 0.00 0.00 30.81 2.59
4269 4820 8.772250 ACCATTCTATCTAGACTTCAAAATGGA 58.228 33.333 23.88 3.86 35.68 3.41
4270 4821 9.618890 CCATTCTATCTAGACTTCAAAATGGAA 57.381 33.333 17.73 6.27 34.78 3.53
4488 5158 7.422399 ACGCCACATATAACAATGAATAAACC 58.578 34.615 0.00 0.00 0.00 3.27
4489 5159 7.067615 ACGCCACATATAACAATGAATAAACCA 59.932 33.333 0.00 0.00 0.00 3.67
4490 5160 7.591057 CGCCACATATAACAATGAATAAACCAG 59.409 37.037 0.00 0.00 0.00 4.00
4491 5161 7.382218 GCCACATATAACAATGAATAAACCAGC 59.618 37.037 0.00 0.00 0.00 4.85
4492 5162 8.412456 CCACATATAACAATGAATAAACCAGCA 58.588 33.333 0.00 0.00 0.00 4.41
4493 5163 9.800433 CACATATAACAATGAATAAACCAGCAA 57.200 29.630 0.00 0.00 0.00 3.91
4558 5228 8.362464 TCTGTAGAAATATCACAAGTACCACT 57.638 34.615 0.00 0.00 0.00 4.00
4560 5230 6.816640 TGTAGAAATATCACAAGTACCACTGC 59.183 38.462 0.00 0.00 0.00 4.40
4564 5234 1.301716 CACAAGTACCACTGCGCCT 60.302 57.895 4.18 0.00 0.00 5.52
4613 5283 6.996282 ACTATACCCAAAATCCTTCATAACCG 59.004 38.462 0.00 0.00 0.00 4.44
4627 5297 5.608676 TCATAACCGCGTGAATTACAAAA 57.391 34.783 4.92 0.00 0.00 2.44
4661 5331 7.731882 AAAGTGCTCTTAAAGTTCTAAGTCC 57.268 36.000 0.66 1.22 33.09 3.85
4667 5337 4.992951 TCTTAAAGTTCTAAGTCCGGTTGC 59.007 41.667 0.00 0.00 31.86 4.17
4735 5447 8.342634 ACGGAAATGATAAATCCTAAATGTTCG 58.657 33.333 0.00 0.00 0.00 3.95
4749 5461 5.337578 AAATGTTCGGATTTTACCCATGG 57.662 39.130 4.14 4.14 0.00 3.66
4750 5462 2.096248 TGTTCGGATTTTACCCATGGC 58.904 47.619 6.09 0.00 0.00 4.40
4794 5506 3.326747 ACTTTAGTTGACGTGAGATGGC 58.673 45.455 0.00 0.00 0.00 4.40
4795 5507 3.244078 ACTTTAGTTGACGTGAGATGGCA 60.244 43.478 0.00 0.00 0.00 4.92
4796 5508 3.394674 TTAGTTGACGTGAGATGGCAA 57.605 42.857 0.00 0.00 0.00 4.52
4797 5509 1.800805 AGTTGACGTGAGATGGCAAG 58.199 50.000 0.00 0.00 0.00 4.01
4802 5514 3.325870 TGACGTGAGATGGCAAGTTTAG 58.674 45.455 0.00 0.00 30.71 1.85
4842 5554 2.938838 TCTGGTGAAAACCAAACCGAT 58.061 42.857 0.00 0.00 39.61 4.18
4884 5596 5.880901 ACCAACTAAACTTGTCATCCTCAT 58.119 37.500 0.00 0.00 0.00 2.90
4949 5661 6.001460 ACAAAATCTGAACATTCGGGACTTA 58.999 36.000 0.66 0.00 34.32 2.24
4951 5663 7.176690 ACAAAATCTGAACATTCGGGACTTATT 59.823 33.333 0.66 0.00 34.32 1.40
5000 6000 4.077300 TCTGGGCTAACTGCTTATGATG 57.923 45.455 0.00 0.00 42.39 3.07
5014 6014 5.465390 TGCTTATGATGGCGTGTATAAAGAC 59.535 40.000 0.00 0.00 0.00 3.01
5016 6016 3.786516 TGATGGCGTGTATAAAGACGA 57.213 42.857 0.00 0.00 44.66 4.20
5038 6038 6.153000 ACGATTAGGAGTGTCATATGGGATAC 59.847 42.308 2.13 0.00 0.00 2.24
5044 6044 7.019388 AGGAGTGTCATATGGGATACAATACT 58.981 38.462 2.13 2.36 39.74 2.12
5065 6065 4.068599 CTGAGGTGAAGGAAAGAAGAACC 58.931 47.826 0.00 0.00 0.00 3.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 3.591254 AAAGCGCCACGGAGGAGAC 62.591 63.158 2.29 0.00 40.01 3.36
17 18 1.120437 GAAAGTTCAAAAGCGCCACG 58.880 50.000 2.29 0.00 0.00 4.94
21 25 1.852280 GGTGTGAAAGTTCAAAAGCGC 59.148 47.619 0.00 0.00 39.21 5.92
23 27 2.098443 TCGGGTGTGAAAGTTCAAAAGC 59.902 45.455 0.00 0.00 39.21 3.51
27 31 2.294074 CCTTCGGGTGTGAAAGTTCAA 58.706 47.619 0.00 0.00 39.21 2.69
50 54 0.950116 GCAGCTTATGGGTGATGAGC 59.050 55.000 4.31 0.00 45.36 4.26
52 56 0.918258 TGGCAGCTTATGGGTGATGA 59.082 50.000 0.00 0.00 45.36 2.92
54 58 0.625316 TGTGGCAGCTTATGGGTGAT 59.375 50.000 0.00 0.00 45.36 3.06
57 61 3.380471 TTTATGTGGCAGCTTATGGGT 57.620 42.857 0.00 0.00 0.00 4.51
59 63 6.152932 AGATTTTTATGTGGCAGCTTATGG 57.847 37.500 0.00 0.00 0.00 2.74
62 66 6.832520 TCAAGATTTTTATGTGGCAGCTTA 57.167 33.333 0.00 0.00 0.00 3.09
74 78 5.177326 GGCATTGGCACATCAAGATTTTTA 58.823 37.500 5.17 0.00 43.71 1.52
75 79 4.004982 GGCATTGGCACATCAAGATTTTT 58.995 39.130 5.17 0.00 43.71 1.94
81 85 1.472552 CCATGGCATTGGCACATCAAG 60.473 52.381 15.84 1.94 41.84 3.02
106 111 3.256631 AGCCAAAATGCCTGAAGTAGTTG 59.743 43.478 0.00 0.00 0.00 3.16
111 116 1.891150 CAGAGCCAAAATGCCTGAAGT 59.109 47.619 0.00 0.00 33.84 3.01
117 122 0.169009 GACGTCAGAGCCAAAATGCC 59.831 55.000 11.55 0.00 0.00 4.40
128 133 5.534654 AGGAAAAATTTGGATTGACGTCAGA 59.465 36.000 19.11 10.37 0.00 3.27
130 135 5.782893 AGGAAAAATTTGGATTGACGTCA 57.217 34.783 15.76 15.76 0.00 4.35
131 136 6.308041 GCTAAGGAAAAATTTGGATTGACGTC 59.692 38.462 9.11 9.11 0.00 4.34
147 152 4.343526 TGATGCCAAAACTTGCTAAGGAAA 59.656 37.500 0.00 0.00 0.00 3.13
148 153 3.894427 TGATGCCAAAACTTGCTAAGGAA 59.106 39.130 0.00 0.00 0.00 3.36
149 154 3.495331 TGATGCCAAAACTTGCTAAGGA 58.505 40.909 0.00 0.00 0.00 3.36
165 170 0.465705 TTCCAGGTCCGATCTGATGC 59.534 55.000 10.44 0.00 34.36 3.91
166 171 1.069823 CCTTCCAGGTCCGATCTGATG 59.930 57.143 10.44 0.15 34.36 3.07
173 178 0.758734 CATATGCCTTCCAGGTCCGA 59.241 55.000 0.00 0.00 37.80 4.55
174 179 0.758734 TCATATGCCTTCCAGGTCCG 59.241 55.000 0.00 0.00 37.80 4.79
176 181 4.646492 ACAAAATCATATGCCTTCCAGGTC 59.354 41.667 0.00 0.00 37.80 3.85
208 213 3.081048 GGGAATCTGGCCCCAAAAA 57.919 52.632 0.00 0.00 42.24 1.94
242 247 2.257691 TCAACGATCCCCACGAAAAA 57.742 45.000 0.00 0.00 34.70 1.94
247 252 1.448985 ACAAATCAACGATCCCCACG 58.551 50.000 0.00 0.00 0.00 4.94
248 253 2.817258 TGAACAAATCAACGATCCCCAC 59.183 45.455 0.00 0.00 34.30 4.61
249 254 3.147553 TGAACAAATCAACGATCCCCA 57.852 42.857 0.00 0.00 34.30 4.96
290 297 8.977505 AGACACCATTTCAAATAATTTTGTTCG 58.022 29.630 0.00 0.00 42.37 3.95
293 300 9.480053 CTCAGACACCATTTCAAATAATTTTGT 57.520 29.630 0.00 0.00 42.37 2.83
311 318 4.243007 CCAAAATTTGGTCCTCAGACAC 57.757 45.455 16.24 0.00 45.48 3.67
335 342 3.427503 CCGTATCTGCCACAATTTTGTCC 60.428 47.826 0.00 0.00 39.91 4.02
338 345 3.190327 TCACCGTATCTGCCACAATTTTG 59.810 43.478 0.00 0.00 0.00 2.44
375 382 3.186702 TGGCATGCATGATCAATTTGG 57.813 42.857 30.64 0.00 0.00 3.28
437 465 1.526575 AAGGCAGAAACCACGGCATG 61.527 55.000 0.00 0.00 33.04 4.06
438 466 0.037590 TAAGGCAGAAACCACGGCAT 59.962 50.000 0.00 0.00 33.04 4.40
439 467 0.887387 GTAAGGCAGAAACCACGGCA 60.887 55.000 0.00 0.00 33.04 5.69
440 468 1.873863 GTAAGGCAGAAACCACGGC 59.126 57.895 0.00 0.00 0.00 5.68
469 497 4.466370 CCCATAATTGATAGGCCGACTCTA 59.534 45.833 0.00 0.00 0.00 2.43
1306 1361 3.244976 CTCTTAAGTTGCCAAATTGCCG 58.755 45.455 0.00 0.00 0.00 5.69
1309 1364 4.874970 ACAGCTCTTAAGTTGCCAAATTG 58.125 39.130 15.69 11.21 37.24 2.32
1362 1417 3.452474 CACAAATTCAAACAAGCCCGAA 58.548 40.909 0.00 0.00 0.00 4.30
1364 1419 1.526464 GCACAAATTCAAACAAGCCCG 59.474 47.619 0.00 0.00 0.00 6.13
1416 1471 4.621747 GCTCATCCACAGCTAGTTTGTACT 60.622 45.833 0.00 0.00 38.44 2.73
1417 1472 3.619038 GCTCATCCACAGCTAGTTTGTAC 59.381 47.826 2.35 0.00 33.75 2.90
1418 1473 3.260632 TGCTCATCCACAGCTAGTTTGTA 59.739 43.478 2.35 0.00 37.79 2.41
1419 1474 2.038952 TGCTCATCCACAGCTAGTTTGT 59.961 45.455 0.00 0.00 37.79 2.83
1452 1507 1.177401 GGTGAAATTCCACTGGAGCC 58.823 55.000 0.00 0.00 37.24 4.70
1462 1517 5.681880 TCGTATTTGAACGTGGTGAAATTC 58.318 37.500 0.00 0.00 43.31 2.17
1466 1521 5.676532 AAATCGTATTTGAACGTGGTGAA 57.323 34.783 0.00 0.00 43.31 3.18
1488 1551 5.290493 AGGCATGGACTCAATTACGATAA 57.710 39.130 0.00 0.00 0.00 1.75
1489 1552 4.955811 AGGCATGGACTCAATTACGATA 57.044 40.909 0.00 0.00 0.00 2.92
1490 1553 3.845781 AGGCATGGACTCAATTACGAT 57.154 42.857 0.00 0.00 0.00 3.73
1514 1577 0.871057 GCACCAGCTCTCAGTTTGAC 59.129 55.000 0.00 0.00 37.91 3.18
1631 1694 4.141869 TGCATCACAGCATATACAGACAGT 60.142 41.667 0.00 0.00 40.11 3.55
1658 1721 7.537596 AGGATGTGTACAAATCCAAAATCAA 57.462 32.000 36.11 0.00 44.17 2.57
1660 1723 8.739972 AGTAAGGATGTGTACAAATCCAAAATC 58.260 33.333 36.11 23.59 44.17 2.17
1662 1725 8.472007 AAGTAAGGATGTGTACAAATCCAAAA 57.528 30.769 36.11 22.64 44.17 2.44
1698 1761 2.037121 TGCTTCCGTTCTGAGTCAATGA 59.963 45.455 0.00 0.00 0.00 2.57
1699 1762 2.414481 CTGCTTCCGTTCTGAGTCAATG 59.586 50.000 0.00 0.00 0.00 2.82
1700 1763 2.300152 TCTGCTTCCGTTCTGAGTCAAT 59.700 45.455 0.00 0.00 0.00 2.57
1747 1810 6.623979 TGGCCCACTGTAAAGTATAAAGTA 57.376 37.500 0.00 0.00 0.00 2.24
1760 1823 1.559682 CTACACCTTATGGCCCACTGT 59.440 52.381 0.00 0.00 36.63 3.55
1794 1857 7.961325 AATGCGGATAAAATCAACAAAACTT 57.039 28.000 0.00 0.00 0.00 2.66
1810 1873 7.264221 TGCACTTTCAAATATTAAATGCGGAT 58.736 30.769 0.00 0.00 33.26 4.18
1813 1876 6.842282 GCATGCACTTTCAAATATTAAATGCG 59.158 34.615 14.21 0.00 33.26 4.73
1823 1886 9.880157 AAGATTTTATAGCATGCACTTTCAAAT 57.120 25.926 21.98 14.90 0.00 2.32
1952 2016 5.807011 AGTTCAAATGTTGCACTCTGAAAAC 59.193 36.000 0.00 0.00 31.45 2.43
2036 2100 8.545472 AGAAATATTACCAAGTAGGCAAGTACA 58.455 33.333 0.00 0.00 43.14 2.90
2043 2107 9.353999 CAAAAACAGAAATATTACCAAGTAGGC 57.646 33.333 0.00 0.00 43.14 3.93
2095 2183 2.159296 TGCTCATCAATTGCTGCACATC 60.159 45.455 0.00 0.00 32.37 3.06
2129 2221 7.624360 TCAGACAAGAAGCTGTTAAGAAAAA 57.376 32.000 0.00 0.00 33.90 1.94
2170 2263 0.107831 GCCCGGATAGCACAATGGTA 59.892 55.000 0.73 0.00 34.60 3.25
2231 2324 3.301274 AGAGGGACTTGCCATAGTAGAC 58.699 50.000 0.00 0.00 41.55 2.59
2256 2349 5.012239 TGTGAGTAACTGTAATACCGAGGT 58.988 41.667 0.00 0.00 0.00 3.85
2258 2351 7.481642 AGAATGTGAGTAACTGTAATACCGAG 58.518 38.462 0.00 0.00 0.00 4.63
2260 2353 8.404000 ACTAGAATGTGAGTAACTGTAATACCG 58.596 37.037 0.00 0.00 0.00 4.02
2298 2434 3.565902 GCAAACCTAGATATGCAAGGTCC 59.434 47.826 7.48 0.00 38.63 4.46
2339 2487 4.202398 ACTTGGCAATGAAGAGAGACAGAA 60.202 41.667 0.00 0.00 0.00 3.02
2369 2517 8.734386 CAAACAAATATCATAGCCTAATCCCTC 58.266 37.037 0.00 0.00 0.00 4.30
2479 2810 8.171840 GCAAGAGAAACAACAGATAAGTCATAC 58.828 37.037 0.00 0.00 0.00 2.39
2541 2875 3.058777 GGCATGCAACACAAAAATTGGAG 60.059 43.478 21.36 0.00 34.12 3.86
2542 2876 2.877168 GGCATGCAACACAAAAATTGGA 59.123 40.909 21.36 0.00 34.12 3.53
2543 2877 2.879646 AGGCATGCAACACAAAAATTGG 59.120 40.909 21.36 0.00 34.12 3.16
2628 2962 6.791887 ATTGCGTCAAGGATAATATGAGTG 57.208 37.500 0.00 0.00 0.00 3.51
2629 2963 6.992123 TGAATTGCGTCAAGGATAATATGAGT 59.008 34.615 0.00 0.00 0.00 3.41
2630 2964 7.425577 TGAATTGCGTCAAGGATAATATGAG 57.574 36.000 0.00 0.00 0.00 2.90
2632 2966 6.574832 CGTTGAATTGCGTCAAGGATAATATG 59.425 38.462 10.19 0.00 43.04 1.78
2639 2973 0.871722 CCGTTGAATTGCGTCAAGGA 59.128 50.000 15.01 0.00 43.04 3.36
2646 2980 1.434555 TAGACCACCGTTGAATTGCG 58.565 50.000 0.00 0.00 0.00 4.85
2673 3008 2.811431 GGCCAAATTAGCACCCAAAAAC 59.189 45.455 0.00 0.00 0.00 2.43
2716 3053 3.387012 TCCTTGATGAGATGACCCATCA 58.613 45.455 9.30 0.00 45.03 3.07
2722 3059 4.629200 GTCACAGTTCCTTGATGAGATGAC 59.371 45.833 0.00 0.00 0.00 3.06
2878 3224 8.827177 AATATTGCAGCCAGAAAATGAATATG 57.173 30.769 0.00 0.00 0.00 1.78
2893 3239 7.218963 GCAAAGTCAAGTAACTAATATTGCAGC 59.781 37.037 0.00 0.00 38.36 5.25
2948 3294 5.136828 ACATCAACAACATGGACAGGTTTA 58.863 37.500 0.00 0.00 32.51 2.01
3149 3519 7.072177 TCTTATTTTTGATCCGTCATGTGAC 57.928 36.000 3.07 3.07 41.47 3.67
3158 3528 3.947834 AGCACCCTCTTATTTTTGATCCG 59.052 43.478 0.00 0.00 0.00 4.18
3248 3619 5.805486 TGTGATGCGAGATAACTGTAAGAAC 59.195 40.000 0.00 0.00 37.43 3.01
3426 3805 8.823220 AGGTTTCTAACTATGCCAATATGTTT 57.177 30.769 0.00 0.00 0.00 2.83
3450 3830 9.846248 GCCCAAGTTAATGCATTATTATTCTAG 57.154 33.333 19.51 6.72 31.57 2.43
3501 3883 8.469200 CAGTAAATAGAGGCAAAATCCATGAAA 58.531 33.333 0.00 0.00 0.00 2.69
3502 3884 7.416664 GCAGTAAATAGAGGCAAAATCCATGAA 60.417 37.037 0.00 0.00 0.00 2.57
3671 4056 0.253160 AGTAGTTGGGGCATCCTCCA 60.253 55.000 0.00 0.00 36.20 3.86
3687 4072 5.336213 CGCTTTAACCTAGTCTGTCCAAGTA 60.336 44.000 0.00 0.00 0.00 2.24
3698 4083 7.824779 AGAATTTGAGAATCGCTTTAACCTAGT 59.175 33.333 0.00 0.00 38.61 2.57
3717 4102 4.599047 TTGTTGGGCCTTGTAGAATTTG 57.401 40.909 4.53 0.00 0.00 2.32
3730 4115 7.114670 GCAAAACAAAAATAATCATTGTTGGGC 59.885 33.333 4.12 7.23 44.15 5.36
3737 4122 9.118300 TGTTCCTGCAAAACAAAAATAATCATT 57.882 25.926 10.93 0.00 33.86 2.57
3749 4134 2.479389 CGAAGCTTGTTCCTGCAAAACA 60.479 45.455 2.10 9.61 34.93 2.83
3816 4201 1.461268 TCCAGGGACACCAAGCTCA 60.461 57.895 0.00 0.00 40.13 4.26
3900 4285 3.038788 TGCTCGACTGCTGAAACATTA 57.961 42.857 0.00 0.00 0.00 1.90
3958 4343 7.379750 AGACATAAACACTACTCTGAAAGGAC 58.620 38.462 0.00 0.00 0.00 3.85
4006 4393 4.794278 TCATCAGGTAAAACTAGTCGCA 57.206 40.909 0.00 0.00 0.00 5.10
4079 4466 1.613925 ACGTCAGTCAAGAGCTAGCAA 59.386 47.619 18.83 0.00 0.00 3.91
4214 4602 1.008538 GCAGCAACAACGAACAGGG 60.009 57.895 0.00 0.00 0.00 4.45
4258 4809 8.122330 GGCTAAACAAACTTTTCCATTTTGAAG 58.878 33.333 0.52 0.00 34.84 3.02
4269 4820 4.937201 CCCTCAGGCTAAACAAACTTTT 57.063 40.909 0.00 0.00 0.00 2.27
4570 5240 2.183679 AGTTTTTCTTGTGGCAACCCA 58.816 42.857 0.00 0.00 39.32 4.51
4571 5241 2.979814 AGTTTTTCTTGTGGCAACCC 57.020 45.000 0.00 0.00 0.00 4.11
4572 5242 5.466819 GGTATAGTTTTTCTTGTGGCAACC 58.533 41.667 0.00 0.00 0.00 3.77
4573 5243 5.010213 TGGGTATAGTTTTTCTTGTGGCAAC 59.990 40.000 0.00 0.00 0.00 4.17
4574 5244 5.141182 TGGGTATAGTTTTTCTTGTGGCAA 58.859 37.500 0.00 0.00 0.00 4.52
4655 5325 1.504359 CGTTTGAGCAACCGGACTTA 58.496 50.000 9.46 0.00 30.65 2.24
4661 5331 1.154225 GCATCCGTTTGAGCAACCG 60.154 57.895 0.00 0.00 30.65 4.44
4667 5337 2.711542 AGGTAAAGGCATCCGTTTGAG 58.288 47.619 0.00 0.00 32.00 3.02
4727 5439 4.382577 GCCATGGGTAAAATCCGAACATTT 60.383 41.667 15.13 0.00 0.00 2.32
4735 5447 3.383185 TCGATTTGCCATGGGTAAAATCC 59.617 43.478 15.13 0.00 40.35 3.01
4774 5486 3.325870 TGCCATCTCACGTCAACTAAAG 58.674 45.455 0.00 0.00 0.00 1.85
4775 5487 3.394674 TGCCATCTCACGTCAACTAAA 57.605 42.857 0.00 0.00 0.00 1.85
4776 5488 3.244078 ACTTGCCATCTCACGTCAACTAA 60.244 43.478 0.00 0.00 0.00 2.24
4777 5489 2.299013 ACTTGCCATCTCACGTCAACTA 59.701 45.455 0.00 0.00 0.00 2.24
4778 5490 1.070758 ACTTGCCATCTCACGTCAACT 59.929 47.619 0.00 0.00 0.00 3.16
4779 5491 1.512926 ACTTGCCATCTCACGTCAAC 58.487 50.000 0.00 0.00 0.00 3.18
4780 5492 2.254546 AACTTGCCATCTCACGTCAA 57.745 45.000 0.00 0.00 0.00 3.18
4781 5493 2.254546 AAACTTGCCATCTCACGTCA 57.745 45.000 0.00 0.00 0.00 4.35
4782 5494 3.326747 ACTAAACTTGCCATCTCACGTC 58.673 45.455 0.00 0.00 0.00 4.34
4783 5495 3.402628 ACTAAACTTGCCATCTCACGT 57.597 42.857 0.00 0.00 0.00 4.49
4784 5496 3.120199 CCAACTAAACTTGCCATCTCACG 60.120 47.826 0.00 0.00 0.00 4.35
4785 5497 3.366374 GCCAACTAAACTTGCCATCTCAC 60.366 47.826 0.00 0.00 0.00 3.51
4786 5498 2.819608 GCCAACTAAACTTGCCATCTCA 59.180 45.455 0.00 0.00 0.00 3.27
4787 5499 2.819608 TGCCAACTAAACTTGCCATCTC 59.180 45.455 0.00 0.00 0.00 2.75
4788 5500 2.875296 TGCCAACTAAACTTGCCATCT 58.125 42.857 0.00 0.00 0.00 2.90
4789 5501 3.578688 CTTGCCAACTAAACTTGCCATC 58.421 45.455 0.00 0.00 0.00 3.51
4790 5502 2.289010 GCTTGCCAACTAAACTTGCCAT 60.289 45.455 0.00 0.00 0.00 4.40
4791 5503 1.068434 GCTTGCCAACTAAACTTGCCA 59.932 47.619 0.00 0.00 0.00 4.92
4792 5504 1.068434 TGCTTGCCAACTAAACTTGCC 59.932 47.619 0.00 0.00 0.00 4.52
4793 5505 2.507339 TGCTTGCCAACTAAACTTGC 57.493 45.000 0.00 0.00 0.00 4.01
4794 5506 3.983344 GTCATGCTTGCCAACTAAACTTG 59.017 43.478 0.00 0.00 0.00 3.16
4795 5507 3.636300 TGTCATGCTTGCCAACTAAACTT 59.364 39.130 0.00 0.00 0.00 2.66
4796 5508 3.221771 TGTCATGCTTGCCAACTAAACT 58.778 40.909 0.00 0.00 0.00 2.66
4797 5509 3.641437 TGTCATGCTTGCCAACTAAAC 57.359 42.857 0.00 0.00 0.00 2.01
4802 5514 4.060205 AGAAAATTGTCATGCTTGCCAAC 58.940 39.130 0.00 0.00 0.00 3.77
4842 5554 6.631314 AGTTGGTAAACATGGCAATTTTGTCA 60.631 34.615 0.00 0.00 39.46 3.58
4933 5645 3.616219 CCCAATAAGTCCCGAATGTTCA 58.384 45.455 0.00 0.00 0.00 3.18
4949 5661 4.938028 ACCTTTTAATTACGGACCCCAAT 58.062 39.130 2.55 0.00 0.00 3.16
4951 5663 4.202545 TGAACCTTTTAATTACGGACCCCA 60.203 41.667 2.55 0.00 0.00 4.96
4959 5671 6.863275 CCAGATGGGTGAACCTTTTAATTAC 58.137 40.000 0.00 0.00 41.11 1.89
4989 5989 5.696270 TCTTTATACACGCCATCATAAGCAG 59.304 40.000 0.00 0.00 0.00 4.24
5000 6000 4.863491 TCCTAATCGTCTTTATACACGCC 58.137 43.478 0.00 0.00 35.93 5.68
5014 6014 5.667539 ATCCCATATGACACTCCTAATCG 57.332 43.478 3.65 0.00 0.00 3.34
5016 6016 7.872061 TTGTATCCCATATGACACTCCTAAT 57.128 36.000 3.65 0.00 0.00 1.73
5038 6038 6.467677 TCTTCTTTCCTTCACCTCAGTATTG 58.532 40.000 0.00 0.00 0.00 1.90
5044 6044 3.458118 TGGTTCTTCTTTCCTTCACCTCA 59.542 43.478 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.