Multiple sequence alignment - TraesCS6B01G283700

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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 TraesCS6B01G283700 chr6B 100.000 2347 0 0 1 2347 512192822 512190476 0.000000e+00 4335.0
1 TraesCS6B01G283700 chr6B 86.645 629 48 18 1 606 587581849 587581234 0.000000e+00 664.0
2 TraesCS6B01G283700 chr6B 88.533 375 22 5 244 599 512199613 512199985 4.370000e-118 435.0
3 TraesCS6B01G283700 chr6B 100.000 204 0 0 2652 2855 512190171 512189968 7.470000e-101 377.0
4 TraesCS6B01G283700 chr6B 84.270 89 13 1 2076 2163 16341436 16341348 5.070000e-13 86.1
5 TraesCS6B01G283700 chr6D 91.081 1693 95 21 602 2268 315360012 315361674 0.000000e+00 2239.0
6 TraesCS6B01G283700 chr6D 91.589 321 22 5 4 321 274443200 274442882 3.380000e-119 438.0
7 TraesCS6B01G283700 chr6D 91.277 321 24 4 4 321 211206296 211206615 4.370000e-118 435.0
8 TraesCS6B01G283700 chr6D 97.500 160 4 0 2696 2855 315361677 315361836 1.010000e-69 274.0
9 TraesCS6B01G283700 chr6D 84.848 66 10 0 2078 2143 369636880 369636945 1.840000e-07 67.6
10 TraesCS6B01G283700 chr6D 85.965 57 8 0 2107 2163 438915021 438914965 8.540000e-06 62.1
11 TraesCS6B01G283700 chr6A 92.876 1137 48 10 637 1743 452275321 452276454 0.000000e+00 1620.0
12 TraesCS6B01G283700 chr6A 91.589 321 23 4 4 321 421169393 421169712 9.390000e-120 440.0
13 TraesCS6B01G283700 chr6A 91.875 160 12 1 2696 2855 452276506 452276664 3.700000e-54 222.0
14 TraesCS6B01G283700 chr6A 80.682 88 17 0 2083 2170 25634500 25634587 5.100000e-08 69.4
15 TraesCS6B01G283700 chr2B 88.455 615 55 8 1 603 211042337 211041727 0.000000e+00 728.0
16 TraesCS6B01G283700 chr2B 85.423 638 52 19 1 611 207999218 207999841 2.420000e-175 625.0
17 TraesCS6B01G283700 chr2B 81.053 95 16 2 2076 2169 247368626 247368533 1.100000e-09 75.0
18 TraesCS6B01G283700 chrUn 88.254 613 52 9 1 601 121745191 121744587 0.000000e+00 715.0
19 TraesCS6B01G283700 chrUn 83.529 85 14 0 2078 2162 50872365 50872449 2.360000e-11 80.5
20 TraesCS6B01G283700 chrUn 83.529 85 14 0 2078 2162 50890277 50890361 2.360000e-11 80.5
21 TraesCS6B01G283700 chr1D 85.965 627 60 10 1 602 465454451 465453828 0.000000e+00 645.0
22 TraesCS6B01G283700 chr1D 85.692 629 58 15 1 599 465456484 465457110 4.010000e-178 634.0
23 TraesCS6B01G283700 chr1D 86.667 75 10 0 2084 2158 410795909 410795983 1.820000e-12 84.2
24 TraesCS6B01G283700 chr1D 95.000 40 2 0 2096 2135 393747474 393747513 2.370000e-06 63.9
25 TraesCS6B01G283700 chr1D 92.308 39 3 0 2101 2139 53260536 53260574 3.970000e-04 56.5
26 TraesCS6B01G283700 chr7A 85.781 640 53 19 1 616 676375821 676375196 0.000000e+00 643.0
27 TraesCS6B01G283700 chr5B 86.013 622 50 19 1 599 126000153 126000760 1.440000e-177 632.0
28 TraesCS6B01G283700 chr3D 85.346 621 62 15 1 599 437185933 437185320 1.450000e-172 616.0
29 TraesCS6B01G283700 chr3D 98.718 78 1 0 2270 2347 341461222 341461145 3.840000e-29 139.0
30 TraesCS6B01G283700 chr3D 83.908 87 12 2 2079 2164 126949045 126949130 6.560000e-12 82.4
31 TraesCS6B01G283700 chr3D 83.721 86 10 4 2082 2163 79508463 79508378 8.480000e-11 78.7
32 TraesCS6B01G283700 chr3D 83.784 74 12 0 2079 2152 582882084 582882157 1.420000e-08 71.3
33 TraesCS6B01G283700 chr3D 80.952 84 16 0 2083 2166 313178332 313178415 1.840000e-07 67.6
34 TraesCS6B01G283700 chr7B 84.804 612 71 13 1 599 236895181 236894579 1.890000e-166 595.0
35 TraesCS6B01G283700 chr2A 84.665 626 59 19 2 603 181541634 181542246 8.810000e-165 590.0
36 TraesCS6B01G283700 chr2A 91.925 322 20 6 4 321 524226782 524226463 2.020000e-121 446.0
37 TraesCS6B01G283700 chr2A 82.222 90 15 1 2076 2164 177658413 177658324 3.050000e-10 76.8
38 TraesCS6B01G283700 chr5D 85.664 565 51 13 57 599 565069198 565069754 4.130000e-158 568.0
39 TraesCS6B01G283700 chr5D 91.900 321 20 6 4 321 366647235 366647552 7.260000e-121 444.0
40 TraesCS6B01G283700 chr5D 87.879 66 8 0 2082 2147 324375001 324375066 8.480000e-11 78.7
41 TraesCS6B01G283700 chr1B 84.656 567 59 15 57 599 642204109 642204671 9.000000e-150 540.0
42 TraesCS6B01G283700 chr3A 91.900 321 22 4 4 321 74399928 74399609 2.020000e-121 446.0
43 TraesCS6B01G283700 chr3A 91.615 322 20 7 4 321 163429834 163430152 3.380000e-119 438.0
44 TraesCS6B01G283700 chr3A 91.304 322 22 6 4 321 463043846 463044165 4.370000e-118 435.0
45 TraesCS6B01G283700 chr3A 86.111 72 10 0 2095 2166 419336165 419336094 8.480000e-11 78.7
46 TraesCS6B01G283700 chr4D 91.277 321 23 5 4 321 342900434 342900116 1.570000e-117 433.0
47 TraesCS6B01G283700 chr4D 84.058 69 11 0 2095 2163 509646372 509646440 1.840000e-07 67.6
48 TraesCS6B01G283700 chr7D 89.236 288 19 4 322 598 276951693 276951407 1.630000e-92 350.0
49 TraesCS6B01G283700 chr7D 80.645 93 13 5 2083 2174 190083224 190083312 1.840000e-07 67.6
50 TraesCS6B01G283700 chr3B 97.368 76 2 0 2270 2345 440116908 440116833 2.310000e-26 130.0
51 TraesCS6B01G283700 chr3B 83.908 87 12 2 2079 2164 181288810 181288895 6.560000e-12 82.4
52 TraesCS6B01G283700 chr5A 83.529 85 14 0 2079 2163 613596519 613596603 2.360000e-11 80.5
53 TraesCS6B01G283700 chr5A 87.500 64 8 0 2101 2164 3397767 3397704 1.100000e-09 75.0
54 TraesCS6B01G283700 chr4A 83.951 81 13 0 2082 2162 662286499 662286419 8.480000e-11 78.7
55 TraesCS6B01G283700 chr2D 82.222 90 15 1 2076 2164 172409662 172409751 3.050000e-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 TraesCS6B01G283700 chr6B 512189968 512192822 2854 True 2356.0 4335 100.0000 1 2855 2 chr6B.!!$R3 2854
1 TraesCS6B01G283700 chr6B 587581234 587581849 615 True 664.0 664 86.6450 1 606 1 chr6B.!!$R2 605
2 TraesCS6B01G283700 chr6D 315360012 315361836 1824 False 1256.5 2239 94.2905 602 2855 2 chr6D.!!$F3 2253
3 TraesCS6B01G283700 chr6A 452275321 452276664 1343 False 921.0 1620 92.3755 637 2855 2 chr6A.!!$F3 2218
4 TraesCS6B01G283700 chr2B 211041727 211042337 610 True 728.0 728 88.4550 1 603 1 chr2B.!!$R1 602
5 TraesCS6B01G283700 chr2B 207999218 207999841 623 False 625.0 625 85.4230 1 611 1 chr2B.!!$F1 610
6 TraesCS6B01G283700 chrUn 121744587 121745191 604 True 715.0 715 88.2540 1 601 1 chrUn.!!$R1 600
7 TraesCS6B01G283700 chr1D 465453828 465454451 623 True 645.0 645 85.9650 1 602 1 chr1D.!!$R1 601
8 TraesCS6B01G283700 chr1D 465456484 465457110 626 False 634.0 634 85.6920 1 599 1 chr1D.!!$F4 598
9 TraesCS6B01G283700 chr7A 676375196 676375821 625 True 643.0 643 85.7810 1 616 1 chr7A.!!$R1 615
10 TraesCS6B01G283700 chr5B 126000153 126000760 607 False 632.0 632 86.0130 1 599 1 chr5B.!!$F1 598
11 TraesCS6B01G283700 chr3D 437185320 437185933 613 True 616.0 616 85.3460 1 599 1 chr3D.!!$R3 598
12 TraesCS6B01G283700 chr7B 236894579 236895181 602 True 595.0 595 84.8040 1 599 1 chr7B.!!$R1 598
13 TraesCS6B01G283700 chr2A 181541634 181542246 612 False 590.0 590 84.6650 2 603 1 chr2A.!!$F1 601
14 TraesCS6B01G283700 chr5D 565069198 565069754 556 False 568.0 568 85.6640 57 599 1 chr5D.!!$F3 542
15 TraesCS6B01G283700 chr1B 642204109 642204671 562 False 540.0 540 84.6560 57 599 1 chr1B.!!$F1 542

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
398 438 0.037326 TGCTCGTGGAGTTGATGGAC 60.037 55.0 0.00 0.0 31.39 4.02 F
1263 1326 0.101759 CGAAAATGCTGGCATCCCTG 59.898 55.0 8.57 0.0 35.31 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1535 1628 0.040646 TAGACTCACATGGTCCCCGT 59.959 55.0 0.00 0.0 34.56 5.28 R
2671 2785 0.385974 AACGAAAATGCTGTCAGCGC 60.386 50.0 19.68 0.0 46.26 5.92 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
32 33 0.248289 ATTAGTCGTGTCCCCGGTTG 59.752 55.000 0.00 0.00 0.00 3.77
73 74 3.452627 AGTAGTGGAAATGCCGAGAGATT 59.547 43.478 0.00 0.00 40.66 2.40
86 87 4.928615 GCCGAGAGATTTCATCATCCTTAG 59.071 45.833 0.00 0.00 0.00 2.18
98 99 9.567776 TTTCATCATCCTTAGTTTAAACAGTGA 57.432 29.630 20.06 13.24 0.00 3.41
100 101 8.593679 TCATCATCCTTAGTTTAAACAGTGAGA 58.406 33.333 20.06 10.10 0.00 3.27
159 172 5.823861 TGCCAACTCATCCTATGCTATTA 57.176 39.130 0.00 0.00 0.00 0.98
339 376 4.546570 CAACTGCAGATATATCCGACGAA 58.453 43.478 23.35 0.00 0.00 3.85
398 438 0.037326 TGCTCGTGGAGTTGATGGAC 60.037 55.000 0.00 0.00 31.39 4.02
447 488 9.206870 CAGTATTTCTTTTATTTGGCATTGTGT 57.793 29.630 0.00 0.00 0.00 3.72
543 595 1.391485 GTGTGTGCTAGCAAGTCGATG 59.609 52.381 21.29 0.00 0.00 3.84
567 619 2.602878 CGACTAGCACGGTAAACACAT 58.397 47.619 0.00 0.00 0.00 3.21
585 637 4.954202 ACACATAGACTTCGATCCTTACCA 59.046 41.667 0.00 0.00 0.00 3.25
702 755 2.042686 TTCTGATTGGAAGGATGGCG 57.957 50.000 0.00 0.00 0.00 5.69
706 759 0.107214 GATTGGAAGGATGGCGGTCA 60.107 55.000 0.00 0.00 0.00 4.02
725 778 7.010552 GGCGGTCATAGCTATATCAGTAATTTG 59.989 40.741 5.77 0.00 34.52 2.32
749 805 7.114754 TGTAAGATGCTCTTTCATGGATTCTT 58.885 34.615 4.15 0.00 37.89 2.52
755 818 7.765695 TGCTCTTTCATGGATTCTTAACTTT 57.234 32.000 0.00 0.00 0.00 2.66
778 841 9.219603 CTTTTATTGACTGTATGAAGAACTCCA 57.780 33.333 0.00 0.00 0.00 3.86
801 864 4.589908 AGGAATGGAAGCGATACAAAAGT 58.410 39.130 0.00 0.00 0.00 2.66
836 899 6.611613 ACAAGAATACTCTGAGGATGTCAA 57.388 37.500 2.46 0.00 33.60 3.18
838 901 7.046652 ACAAGAATACTCTGAGGATGTCAATG 58.953 38.462 2.46 8.87 33.60 2.82
877 940 0.631753 TGTAGAGCCTAGCAGGGAGT 59.368 55.000 4.65 0.00 35.37 3.85
915 978 1.227645 GGCATGCTGTCGGCTATGA 60.228 57.895 18.92 0.00 42.39 2.15
948 1011 1.558233 ACCGTCTCCTTCCTGGTAAG 58.442 55.000 0.00 0.00 37.07 2.34
1187 1250 4.523943 TGCTAGAAGTGCACCAATCAAATT 59.476 37.500 14.63 0.00 35.31 1.82
1244 1307 1.971357 TCAGGACCAGAAGGACTTCAC 59.029 52.381 13.94 3.31 41.84 3.18
1252 1315 3.365364 CCAGAAGGACTTCACGAAAATGC 60.365 47.826 13.94 0.00 41.84 3.56
1253 1316 3.499918 CAGAAGGACTTCACGAAAATGCT 59.500 43.478 13.94 0.00 41.84 3.79
1254 1317 3.499918 AGAAGGACTTCACGAAAATGCTG 59.500 43.478 13.94 0.00 41.84 4.41
1255 1318 2.154462 AGGACTTCACGAAAATGCTGG 58.846 47.619 0.00 0.00 0.00 4.85
1256 1319 1.401539 GGACTTCACGAAAATGCTGGC 60.402 52.381 0.00 0.00 0.00 4.85
1257 1320 1.266718 GACTTCACGAAAATGCTGGCA 59.733 47.619 0.00 0.00 0.00 4.92
1258 1321 1.888512 ACTTCACGAAAATGCTGGCAT 59.111 42.857 1.86 1.86 38.46 4.40
1259 1322 2.095059 ACTTCACGAAAATGCTGGCATC 60.095 45.455 8.57 0.00 35.31 3.91
1260 1323 0.810648 TCACGAAAATGCTGGCATCC 59.189 50.000 8.57 1.42 35.31 3.51
1261 1324 0.179129 CACGAAAATGCTGGCATCCC 60.179 55.000 8.57 1.10 35.31 3.85
1262 1325 0.323725 ACGAAAATGCTGGCATCCCT 60.324 50.000 8.57 0.00 35.31 4.20
1263 1326 0.101759 CGAAAATGCTGGCATCCCTG 59.898 55.000 8.57 0.00 35.31 4.45
1264 1327 1.188863 GAAAATGCTGGCATCCCTGT 58.811 50.000 8.57 0.00 35.31 4.00
1265 1328 0.899720 AAAATGCTGGCATCCCTGTG 59.100 50.000 8.57 0.00 35.31 3.66
1266 1329 0.974010 AAATGCTGGCATCCCTGTGG 60.974 55.000 8.57 0.00 35.31 4.17
1267 1330 2.159101 AATGCTGGCATCCCTGTGGT 62.159 55.000 8.57 0.00 35.31 4.16
1544 1637 3.181431 TTTCCAAAGAAATACGGGGACCA 60.181 43.478 0.00 0.00 42.90 4.02
1545 1638 4.509482 TTTCCAAAGAAATACGGGGACCAT 60.509 41.667 0.00 0.00 42.90 3.55
1559 1652 4.696479 GGGACCATGTGAGTCTATGATT 57.304 45.455 8.84 0.00 34.56 2.57
1592 1685 8.840833 ACATGGCATATGTTTATATCGTAACA 57.159 30.769 0.00 0.00 38.50 2.41
1693 1805 5.499313 TGAAATCTGTATCCAGCACATTGA 58.501 37.500 0.00 0.00 38.66 2.57
1698 1810 2.689471 TGTATCCAGCACATTGATTGGC 59.311 45.455 0.00 0.00 0.00 4.52
1722 1834 2.414481 CAGTCCTGAGTTTGAGATTGCG 59.586 50.000 0.00 0.00 0.00 4.85
1743 1855 0.319555 TCTACACGCGCTGCTTCTTT 60.320 50.000 5.73 0.00 0.00 2.52
1788 1900 2.079158 CATGTGGGTCCATATGCGATC 58.921 52.381 12.58 0.00 38.37 3.69
1860 1972 3.669536 TGTCGCAGAACATTGATGGTTA 58.330 40.909 0.00 0.00 39.69 2.85
1880 1992 2.345760 GGTGGCCACATGCTGAAGG 61.346 63.158 35.78 0.00 40.92 3.46
1881 1993 1.604593 GTGGCCACATGCTGAAGGT 60.605 57.895 31.23 0.00 40.92 3.50
1900 2012 4.070716 AGGTCAGCAATCTTCTGTTTCTG 58.929 43.478 0.00 0.00 33.48 3.02
1919 2031 3.256383 TCTGGATTGCTGGTCATTTTGTG 59.744 43.478 0.00 0.00 0.00 3.33
1955 2067 9.685276 ATGTACATATTCAACTCATTTTCCTCA 57.315 29.630 6.56 0.00 0.00 3.86
1965 2077 8.477256 TCAACTCATTTTCCTCAACTGAAAAAT 58.523 29.630 2.70 0.00 42.91 1.82
1972 2084 7.945033 TTTCCTCAACTGAAAAATAATGTGC 57.055 32.000 0.00 0.00 0.00 4.57
1992 2104 4.928615 GTGCTGTTTAATAATTTGCTGCCA 59.071 37.500 0.00 0.00 0.00 4.92
2088 2201 2.167693 TCGTTGGGCAATAGTACCTCTG 59.832 50.000 0.00 0.00 0.00 3.35
2092 2205 5.681639 GTTGGGCAATAGTACCTCTGTAAT 58.318 41.667 0.00 0.00 0.00 1.89
2099 2212 8.290325 GGCAATAGTACCTCTGTAATTTAATGC 58.710 37.037 0.00 0.00 0.00 3.56
2123 2236 7.886191 CAAGACATTTTTGCAGTTCAATTTG 57.114 32.000 0.00 0.00 34.12 2.32
2124 2237 7.686519 CAAGACATTTTTGCAGTTCAATTTGA 58.313 30.769 0.00 0.00 34.12 2.69
2197 2310 5.398603 TCCTTTCTTCTTCTAGCAGACAG 57.601 43.478 0.00 0.00 0.00 3.51
2268 2382 1.940613 GAGGGCATACTTACTTTGGCG 59.059 52.381 0.00 0.00 36.84 5.69
2269 2383 1.021968 GGGCATACTTACTTTGGCGG 58.978 55.000 0.00 0.00 36.84 6.13
2270 2384 1.021968 GGCATACTTACTTTGGCGGG 58.978 55.000 0.00 0.00 0.00 6.13
2271 2385 1.021968 GCATACTTACTTTGGCGGGG 58.978 55.000 0.00 0.00 0.00 5.73
2272 2386 1.021968 CATACTTACTTTGGCGGGGC 58.978 55.000 0.00 0.00 0.00 5.80
2273 2387 0.621609 ATACTTACTTTGGCGGGGCA 59.378 50.000 0.00 0.00 0.00 5.36
2274 2388 0.400975 TACTTACTTTGGCGGGGCAA 59.599 50.000 3.29 3.29 0.00 4.52
2275 2389 0.893727 ACTTACTTTGGCGGGGCAAG 60.894 55.000 7.73 5.55 0.00 4.01
2276 2390 2.212900 CTTACTTTGGCGGGGCAAGC 62.213 60.000 7.73 0.00 0.00 4.01
2277 2391 2.706952 TTACTTTGGCGGGGCAAGCT 62.707 55.000 7.73 0.63 34.52 3.74
2278 2392 2.706952 TACTTTGGCGGGGCAAGCTT 62.707 55.000 7.73 0.00 34.52 3.74
2279 2393 1.976474 CTTTGGCGGGGCAAGCTTA 60.976 57.895 0.00 0.00 34.52 3.09
2280 2394 1.304879 TTTGGCGGGGCAAGCTTAT 60.305 52.632 0.00 0.00 34.52 1.73
2281 2395 0.902516 TTTGGCGGGGCAAGCTTATT 60.903 50.000 0.00 0.00 34.52 1.40
2282 2396 1.603236 TTGGCGGGGCAAGCTTATTG 61.603 55.000 0.00 0.00 34.52 1.90
2283 2397 2.104928 GCGGGGCAAGCTTATTGC 59.895 61.111 0.00 0.00 44.22 3.56
2297 2411 5.880054 GCTTATTGCTGTTTAGACCAAGA 57.120 39.130 0.00 0.00 38.95 3.02
2298 2412 5.873732 GCTTATTGCTGTTTAGACCAAGAG 58.126 41.667 0.00 0.00 38.95 2.85
2299 2413 5.643777 GCTTATTGCTGTTTAGACCAAGAGA 59.356 40.000 0.00 0.00 38.95 3.10
2300 2414 6.183360 GCTTATTGCTGTTTAGACCAAGAGAG 60.183 42.308 0.00 0.00 38.95 3.20
2301 2415 3.045601 TGCTGTTTAGACCAAGAGAGC 57.954 47.619 0.00 0.00 0.00 4.09
2302 2416 2.289694 TGCTGTTTAGACCAAGAGAGCC 60.290 50.000 0.00 0.00 0.00 4.70
2303 2417 2.027653 GCTGTTTAGACCAAGAGAGCCT 60.028 50.000 0.00 0.00 0.00 4.58
2304 2418 3.594134 CTGTTTAGACCAAGAGAGCCTG 58.406 50.000 0.00 0.00 0.00 4.85
2305 2419 3.239449 TGTTTAGACCAAGAGAGCCTGA 58.761 45.455 0.00 0.00 0.00 3.86
2306 2420 3.006967 TGTTTAGACCAAGAGAGCCTGAC 59.993 47.826 0.00 0.00 0.00 3.51
2307 2421 2.909504 TAGACCAAGAGAGCCTGACT 57.090 50.000 0.00 0.00 0.00 3.41
2308 2422 2.909504 AGACCAAGAGAGCCTGACTA 57.090 50.000 0.00 0.00 0.00 2.59
2309 2423 3.176924 AGACCAAGAGAGCCTGACTAA 57.823 47.619 0.00 0.00 0.00 2.24
2310 2424 3.096092 AGACCAAGAGAGCCTGACTAAG 58.904 50.000 0.00 0.00 0.00 2.18
2323 2437 3.257127 CCTGACTAAGGGATAGTGCTAGC 59.743 52.174 8.10 8.10 45.00 3.42
2324 2438 2.885266 TGACTAAGGGATAGTGCTAGCG 59.115 50.000 10.77 0.00 45.00 4.26
2325 2439 2.229302 GACTAAGGGATAGTGCTAGCGG 59.771 54.545 10.77 0.00 45.00 5.52
2326 2440 2.240279 CTAAGGGATAGTGCTAGCGGT 58.760 52.381 10.77 1.68 0.00 5.68
2327 2441 2.376695 AAGGGATAGTGCTAGCGGTA 57.623 50.000 10.77 4.19 0.00 4.02
2328 2442 1.912417 AGGGATAGTGCTAGCGGTAG 58.088 55.000 17.24 17.24 0.00 3.18
2329 2443 1.145325 AGGGATAGTGCTAGCGGTAGT 59.855 52.381 21.77 6.04 0.00 2.73
2330 2444 1.962100 GGGATAGTGCTAGCGGTAGTT 59.038 52.381 21.77 11.10 0.00 2.24
2331 2445 3.152341 GGGATAGTGCTAGCGGTAGTTA 58.848 50.000 21.77 12.72 0.00 2.24
2332 2446 3.571401 GGGATAGTGCTAGCGGTAGTTAA 59.429 47.826 21.77 6.62 0.00 2.01
2333 2447 4.220163 GGGATAGTGCTAGCGGTAGTTAAT 59.780 45.833 21.77 13.27 0.00 1.40
2334 2448 5.162075 GGATAGTGCTAGCGGTAGTTAATG 58.838 45.833 21.77 0.00 0.00 1.90
2335 2449 3.454371 AGTGCTAGCGGTAGTTAATGG 57.546 47.619 21.77 0.00 0.00 3.16
2336 2450 2.764572 AGTGCTAGCGGTAGTTAATGGT 59.235 45.455 21.77 0.00 0.00 3.55
2337 2451 2.864343 GTGCTAGCGGTAGTTAATGGTG 59.136 50.000 21.77 0.00 0.00 4.17
2338 2452 2.761767 TGCTAGCGGTAGTTAATGGTGA 59.238 45.455 21.77 0.00 0.00 4.02
2339 2453 3.386726 TGCTAGCGGTAGTTAATGGTGAT 59.613 43.478 21.77 0.00 0.00 3.06
2340 2454 4.141801 TGCTAGCGGTAGTTAATGGTGATT 60.142 41.667 21.77 0.00 0.00 2.57
2341 2455 4.211374 GCTAGCGGTAGTTAATGGTGATTG 59.789 45.833 21.77 0.00 0.00 2.67
2342 2456 3.541632 AGCGGTAGTTAATGGTGATTGG 58.458 45.455 0.00 0.00 0.00 3.16
2343 2457 2.032924 GCGGTAGTTAATGGTGATTGGC 59.967 50.000 0.00 0.00 0.00 4.52
2344 2458 2.616842 CGGTAGTTAATGGTGATTGGCC 59.383 50.000 0.00 0.00 0.00 5.36
2345 2459 2.956333 GGTAGTTAATGGTGATTGGCCC 59.044 50.000 0.00 0.00 0.00 5.80
2346 2460 2.917713 AGTTAATGGTGATTGGCCCA 57.082 45.000 0.00 0.00 34.66 5.36
2673 2787 4.232221 ACATTTTCAATGAGAAAGCTGCG 58.768 39.130 3.47 0.00 46.24 5.18
2674 2788 2.336554 TTTCAATGAGAAAGCTGCGC 57.663 45.000 0.00 0.00 41.17 6.09
2675 2789 1.527034 TTCAATGAGAAAGCTGCGCT 58.473 45.000 9.73 0.00 42.56 5.92
2676 2790 0.800631 TCAATGAGAAAGCTGCGCTG 59.199 50.000 9.73 10.04 39.62 5.18
2677 2791 0.800631 CAATGAGAAAGCTGCGCTGA 59.199 50.000 19.32 0.00 39.62 4.26
2678 2792 0.801251 AATGAGAAAGCTGCGCTGAC 59.199 50.000 19.32 9.37 39.62 3.51
2679 2793 0.321034 ATGAGAAAGCTGCGCTGACA 60.321 50.000 19.32 7.63 39.62 3.58
2680 2794 0.947660 TGAGAAAGCTGCGCTGACAG 60.948 55.000 19.32 2.87 39.62 3.51
2687 2801 3.011513 CTGCGCTGACAGCATTTTC 57.988 52.632 26.32 10.25 42.58 2.29
2688 2802 0.791983 CTGCGCTGACAGCATTTTCG 60.792 55.000 26.32 10.49 42.58 3.46
2689 2803 1.207593 GCGCTGACAGCATTTTCGT 59.792 52.632 26.32 0.00 42.58 3.85
2690 2804 0.385974 GCGCTGACAGCATTTTCGTT 60.386 50.000 26.32 0.00 42.58 3.85
2691 2805 1.136085 GCGCTGACAGCATTTTCGTTA 60.136 47.619 26.32 0.00 42.58 3.18
2692 2806 2.664424 GCGCTGACAGCATTTTCGTTAA 60.664 45.455 26.32 0.00 42.58 2.01
2693 2807 3.550561 CGCTGACAGCATTTTCGTTAAA 58.449 40.909 26.32 0.00 42.58 1.52
2694 2808 3.971871 CGCTGACAGCATTTTCGTTAAAA 59.028 39.130 26.32 0.00 42.58 1.52
2806 2920 8.685536 CAAAGCGCTTATTCATTAATCTTTAGC 58.314 33.333 25.33 0.00 0.00 3.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 2.939103 ACTAGATGCTCAATTTGTCCGC 59.061 45.455 0.00 0.00 0.00 5.54
73 74 9.219603 CTCACTGTTTAAACTAAGGATGATGAA 57.780 33.333 18.72 0.00 0.00 2.57
225 246 1.070601 GCAATTTGGCTGGTGGAAAGT 59.929 47.619 0.00 0.00 0.00 2.66
339 376 3.644884 CGACCTATCGCACCTTAATCT 57.355 47.619 0.00 0.00 42.43 2.40
398 438 3.306166 CGGAAGCAACGTAGTAAATGAGG 59.694 47.826 0.00 0.00 45.00 3.86
429 469 9.590451 AAGATATGACACAATGCCAAATAAAAG 57.410 29.630 0.00 0.00 0.00 2.27
543 595 0.734942 TTTACCGTGCTAGTCGCTGC 60.735 55.000 0.00 0.00 40.11 5.25
547 599 2.054687 TGTGTTTACCGTGCTAGTCG 57.945 50.000 0.00 0.00 0.00 4.18
562 614 4.954202 TGGTAAGGATCGAAGTCTATGTGT 59.046 41.667 0.00 0.00 0.00 3.72
585 637 1.749638 CTGTCTAGCGACCCGACCT 60.750 63.158 0.00 0.00 39.47 3.85
659 711 6.761731 TTTTCAAATGGTATGCAACTTTCG 57.238 33.333 0.00 0.00 0.00 3.46
755 818 7.824289 CCTTGGAGTTCTTCATACAGTCAATAA 59.176 37.037 0.00 0.00 0.00 1.40
778 841 5.010282 ACTTTTGTATCGCTTCCATTCCTT 58.990 37.500 0.00 0.00 0.00 3.36
801 864 5.544176 AGAGTATTCTTGTTCAGAAGGTGGA 59.456 40.000 0.00 0.00 45.11 4.02
877 940 4.766373 TGCCTTTGACAAATGATTGAGCTA 59.234 37.500 7.32 0.00 38.94 3.32
915 978 0.318762 GACGGTTCAGGTCAAGCTCT 59.681 55.000 0.00 0.00 34.56 4.09
948 1011 2.351726 GCCACATTCGATTGTGTAGTCC 59.648 50.000 28.86 14.10 44.42 3.85
1244 1307 0.101759 CAGGGATGCCAGCATTTTCG 59.898 55.000 5.86 0.00 36.70 3.46
1252 1315 0.251297 TCAAACCACAGGGATGCCAG 60.251 55.000 5.86 0.00 38.05 4.85
1253 1316 0.409092 ATCAAACCACAGGGATGCCA 59.591 50.000 5.86 0.00 38.05 4.92
1254 1317 1.560505 AATCAAACCACAGGGATGCC 58.439 50.000 0.00 0.00 38.05 4.40
1255 1318 2.299867 ACAAATCAAACCACAGGGATGC 59.700 45.455 0.00 0.00 38.05 3.91
1256 1319 5.394443 CCATACAAATCAAACCACAGGGATG 60.394 44.000 0.00 0.00 38.05 3.51
1257 1320 4.711355 CCATACAAATCAAACCACAGGGAT 59.289 41.667 0.00 0.00 38.05 3.85
1258 1321 4.085733 CCATACAAATCAAACCACAGGGA 58.914 43.478 0.00 0.00 38.05 4.20
1259 1322 4.085733 TCCATACAAATCAAACCACAGGG 58.914 43.478 0.00 0.00 41.29 4.45
1260 1323 5.336690 CCTTCCATACAAATCAAACCACAGG 60.337 44.000 0.00 0.00 0.00 4.00
1261 1324 5.336690 CCCTTCCATACAAATCAAACCACAG 60.337 44.000 0.00 0.00 0.00 3.66
1262 1325 4.526262 CCCTTCCATACAAATCAAACCACA 59.474 41.667 0.00 0.00 0.00 4.17
1263 1326 4.081697 CCCCTTCCATACAAATCAAACCAC 60.082 45.833 0.00 0.00 0.00 4.16
1264 1327 4.093011 CCCCTTCCATACAAATCAAACCA 58.907 43.478 0.00 0.00 0.00 3.67
1265 1328 4.081697 CACCCCTTCCATACAAATCAAACC 60.082 45.833 0.00 0.00 0.00 3.27
1266 1329 4.081697 CCACCCCTTCCATACAAATCAAAC 60.082 45.833 0.00 0.00 0.00 2.93
1267 1330 4.093011 CCACCCCTTCCATACAAATCAAA 58.907 43.478 0.00 0.00 0.00 2.69
1360 1448 2.037641 TGTGGAAGTCTGTGACCTCATG 59.962 50.000 0.00 0.00 32.18 3.07
1388 1481 7.592938 TGAAATAACACAATAACTTGCCTGAG 58.407 34.615 0.00 0.00 35.69 3.35
1535 1628 0.040646 TAGACTCACATGGTCCCCGT 59.959 55.000 0.00 0.00 34.56 5.28
1544 1637 9.842775 ATGTATGTTCAAATCATAGACTCACAT 57.157 29.630 0.00 0.00 0.00 3.21
1545 1638 9.101655 CATGTATGTTCAAATCATAGACTCACA 57.898 33.333 0.00 0.00 0.00 3.58
1592 1685 4.380233 GCAGACAAGCAATTCAGCATAAGT 60.380 41.667 0.00 0.00 36.85 2.24
1693 1805 0.687354 AACTCAGGACTGACGCCAAT 59.313 50.000 0.00 0.00 35.46 3.16
1698 1810 3.584406 ATCTCAAACTCAGGACTGACG 57.416 47.619 0.00 0.00 35.46 4.35
1722 1834 2.793322 GAAGCAGCGCGTGTAGAGC 61.793 63.158 8.43 3.15 46.45 4.09
1733 1845 0.803740 CTCTCCAGCAAAGAAGCAGC 59.196 55.000 0.00 0.00 36.85 5.25
1743 1855 4.660303 ACATGGTTATTATCCTCTCCAGCA 59.340 41.667 0.00 0.00 0.00 4.41
1788 1900 3.376234 CCATCCTGTAGCACTTGATGTTG 59.624 47.826 0.00 0.00 32.78 3.33
1860 1972 0.968901 CTTCAGCATGTGGCCACCAT 60.969 55.000 32.62 21.85 46.50 3.55
1880 1992 4.067896 TCCAGAAACAGAAGATTGCTGAC 58.932 43.478 0.00 0.00 36.86 3.51
1881 1993 4.356405 TCCAGAAACAGAAGATTGCTGA 57.644 40.909 0.00 0.00 36.86 4.26
1887 1999 4.015084 CCAGCAATCCAGAAACAGAAGAT 58.985 43.478 0.00 0.00 0.00 2.40
1890 2002 3.149196 GACCAGCAATCCAGAAACAGAA 58.851 45.455 0.00 0.00 0.00 3.02
1900 2012 3.940209 TCACAAAATGACCAGCAATCC 57.060 42.857 0.00 0.00 29.99 3.01
1919 2031 8.879342 AGTTGAATATGTACATCAGTAGCTTC 57.121 34.615 12.68 6.14 0.00 3.86
1965 2077 7.277539 GGCAGCAAATTATTAAACAGCACATTA 59.722 33.333 0.00 0.00 0.00 1.90
1972 2084 7.599630 AACATGGCAGCAAATTATTAAACAG 57.400 32.000 0.00 0.00 0.00 3.16
1992 2104 7.870509 ACATCATAAGTGCATCTTGTAACAT 57.129 32.000 10.59 0.00 37.56 2.71
2061 2174 4.023021 GGTACTATTGCCCAACGACAAAAA 60.023 41.667 0.00 0.00 0.00 1.94
2080 2193 8.263940 TGTCTTGCATTAAATTACAGAGGTAC 57.736 34.615 0.00 0.00 0.00 3.34
2099 2212 7.686519 TCAAATTGAACTGCAAAAATGTCTTG 58.313 30.769 0.00 0.00 40.48 3.02
2141 2254 9.490379 CAAAGTACTTCCTCAGTAACTTAACAT 57.510 33.333 8.95 0.00 39.86 2.71
2142 2255 8.480501 ACAAAGTACTTCCTCAGTAACTTAACA 58.519 33.333 8.95 0.00 39.86 2.41
2143 2256 8.883954 ACAAAGTACTTCCTCAGTAACTTAAC 57.116 34.615 8.95 0.00 39.86 2.01
2153 2266 6.497259 AGGAACAGATACAAAGTACTTCCTCA 59.503 38.462 8.95 0.00 30.06 3.86
2166 2279 7.039011 TGCTAGAAGAAGAAAGGAACAGATACA 60.039 37.037 0.00 0.00 0.00 2.29
2275 2389 5.643777 TCTCTTGGTCTAAACAGCAATAAGC 59.356 40.000 0.00 0.00 46.19 3.09
2276 2390 6.183360 GCTCTCTTGGTCTAAACAGCAATAAG 60.183 42.308 0.00 0.00 33.42 1.73
2277 2391 5.643777 GCTCTCTTGGTCTAAACAGCAATAA 59.356 40.000 0.00 0.00 33.42 1.40
2278 2392 5.178797 GCTCTCTTGGTCTAAACAGCAATA 58.821 41.667 0.00 0.00 33.42 1.90
2279 2393 4.006319 GCTCTCTTGGTCTAAACAGCAAT 58.994 43.478 0.00 0.00 33.42 3.56
2280 2394 3.403038 GCTCTCTTGGTCTAAACAGCAA 58.597 45.455 0.00 0.00 32.88 3.91
2281 2395 2.289694 GGCTCTCTTGGTCTAAACAGCA 60.290 50.000 0.00 0.00 0.00 4.41
2282 2396 2.027653 AGGCTCTCTTGGTCTAAACAGC 60.028 50.000 0.00 0.00 0.00 4.40
2283 2397 3.259374 TCAGGCTCTCTTGGTCTAAACAG 59.741 47.826 0.00 0.00 0.00 3.16
2284 2398 3.006967 GTCAGGCTCTCTTGGTCTAAACA 59.993 47.826 0.00 0.00 0.00 2.83
2285 2399 3.259625 AGTCAGGCTCTCTTGGTCTAAAC 59.740 47.826 0.00 0.00 0.00 2.01
2286 2400 3.511477 AGTCAGGCTCTCTTGGTCTAAA 58.489 45.455 0.00 0.00 0.00 1.85
2287 2401 3.176924 AGTCAGGCTCTCTTGGTCTAA 57.823 47.619 0.00 0.00 0.00 2.10
2288 2402 2.909504 AGTCAGGCTCTCTTGGTCTA 57.090 50.000 0.00 0.00 0.00 2.59
2289 2403 2.909504 TAGTCAGGCTCTCTTGGTCT 57.090 50.000 0.00 0.00 0.00 3.85
2290 2404 2.167487 CCTTAGTCAGGCTCTCTTGGTC 59.833 54.545 0.00 0.00 35.13 4.02
2291 2405 2.183679 CCTTAGTCAGGCTCTCTTGGT 58.816 52.381 0.00 0.00 35.13 3.67
2292 2406 1.484240 CCCTTAGTCAGGCTCTCTTGG 59.516 57.143 0.00 0.00 42.29 3.61
2293 2407 2.461695 TCCCTTAGTCAGGCTCTCTTG 58.538 52.381 0.00 0.00 42.29 3.02
2294 2408 2.930109 TCCCTTAGTCAGGCTCTCTT 57.070 50.000 0.00 0.00 42.29 2.85
2295 2409 3.465588 ACTATCCCTTAGTCAGGCTCTCT 59.534 47.826 0.00 0.00 42.29 3.10
2296 2410 3.572255 CACTATCCCTTAGTCAGGCTCTC 59.428 52.174 0.00 0.00 42.29 3.20
2297 2411 3.571590 CACTATCCCTTAGTCAGGCTCT 58.428 50.000 0.00 0.00 42.29 4.09
2298 2412 2.036604 GCACTATCCCTTAGTCAGGCTC 59.963 54.545 0.00 0.00 42.29 4.70
2299 2413 2.043227 GCACTATCCCTTAGTCAGGCT 58.957 52.381 0.00 0.00 42.29 4.58
2300 2414 2.043227 AGCACTATCCCTTAGTCAGGC 58.957 52.381 0.00 0.00 42.29 4.85
2301 2415 3.257127 GCTAGCACTATCCCTTAGTCAGG 59.743 52.174 10.63 0.00 39.19 3.86
2302 2416 3.057876 CGCTAGCACTATCCCTTAGTCAG 60.058 52.174 16.45 0.00 39.19 3.51
2303 2417 2.885266 CGCTAGCACTATCCCTTAGTCA 59.115 50.000 16.45 0.00 39.19 3.41
2304 2418 2.229302 CCGCTAGCACTATCCCTTAGTC 59.771 54.545 16.45 0.00 39.19 2.59
2305 2419 2.240279 CCGCTAGCACTATCCCTTAGT 58.760 52.381 16.45 0.00 42.04 2.24
2306 2420 2.240279 ACCGCTAGCACTATCCCTTAG 58.760 52.381 16.45 0.00 0.00 2.18
2307 2421 2.376695 ACCGCTAGCACTATCCCTTA 57.623 50.000 16.45 0.00 0.00 2.69
2308 2422 2.240279 CTACCGCTAGCACTATCCCTT 58.760 52.381 16.45 0.00 0.00 3.95
2309 2423 1.145325 ACTACCGCTAGCACTATCCCT 59.855 52.381 16.45 0.00 0.00 4.20
2310 2424 1.618487 ACTACCGCTAGCACTATCCC 58.382 55.000 16.45 0.00 0.00 3.85
2311 2425 4.843220 TTAACTACCGCTAGCACTATCC 57.157 45.455 16.45 0.00 0.00 2.59
2312 2426 5.162075 CCATTAACTACCGCTAGCACTATC 58.838 45.833 16.45 0.00 0.00 2.08
2313 2427 4.587684 ACCATTAACTACCGCTAGCACTAT 59.412 41.667 16.45 0.00 0.00 2.12
2314 2428 3.956199 ACCATTAACTACCGCTAGCACTA 59.044 43.478 16.45 1.78 0.00 2.74
2315 2429 2.764572 ACCATTAACTACCGCTAGCACT 59.235 45.455 16.45 0.47 0.00 4.40
2316 2430 2.864343 CACCATTAACTACCGCTAGCAC 59.136 50.000 16.45 0.00 0.00 4.40
2317 2431 2.761767 TCACCATTAACTACCGCTAGCA 59.238 45.455 16.45 0.00 0.00 3.49
2318 2432 3.447918 TCACCATTAACTACCGCTAGC 57.552 47.619 4.06 4.06 0.00 3.42
2319 2433 4.750098 CCAATCACCATTAACTACCGCTAG 59.250 45.833 0.00 0.00 0.00 3.42
2320 2434 4.699637 CCAATCACCATTAACTACCGCTA 58.300 43.478 0.00 0.00 0.00 4.26
2321 2435 3.541632 CCAATCACCATTAACTACCGCT 58.458 45.455 0.00 0.00 0.00 5.52
2322 2436 2.032924 GCCAATCACCATTAACTACCGC 59.967 50.000 0.00 0.00 0.00 5.68
2323 2437 2.616842 GGCCAATCACCATTAACTACCG 59.383 50.000 0.00 0.00 0.00 4.02
2324 2438 2.956333 GGGCCAATCACCATTAACTACC 59.044 50.000 4.39 0.00 0.00 3.18
2325 2439 3.626930 TGGGCCAATCACCATTAACTAC 58.373 45.455 2.13 0.00 0.00 2.73
2327 2441 2.917713 TGGGCCAATCACCATTAACT 57.082 45.000 2.13 0.00 0.00 2.24
2651 2765 4.232221 CGCAGCTTTCTCATTGAAAATGT 58.768 39.130 0.26 0.00 43.25 2.71
2652 2766 4.817987 CGCAGCTTTCTCATTGAAAATG 57.182 40.909 0.00 0.00 43.25 2.32
2669 2783 0.791983 CGAAAATGCTGTCAGCGCAG 60.792 55.000 19.68 0.00 46.26 5.18
2670 2784 1.207339 CGAAAATGCTGTCAGCGCA 59.793 52.632 19.68 4.73 46.26 6.09
2671 2785 0.385974 AACGAAAATGCTGTCAGCGC 60.386 50.000 19.68 0.00 46.26 5.92
2672 2786 2.873170 TAACGAAAATGCTGTCAGCG 57.127 45.000 19.68 6.95 46.26 5.18
2673 2787 5.881637 TTTTTAACGAAAATGCTGTCAGC 57.118 34.783 18.32 18.32 35.59 4.26
2734 2848 7.507956 TCATTTCATGCTTCCCATTCTTGATAT 59.492 33.333 0.00 0.00 29.71 1.63
2763 2877 4.386049 CGCTTTGAGTTCCTACTTGTACAG 59.614 45.833 0.00 0.00 33.84 2.74


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

AutoCloner maintained by Alex Coulton.