Multiple sequence alignment - TraesCS3D01G147900

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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 TraesCS3D01G147900 chr3D 100.000 4035 0 0 1 4035 112690895 112694929 0.000000e+00 7452.0
1 TraesCS3D01G147900 chr3D 92.135 89 6 1 31 119 405817978 405817891 1.520000e-24 124.0
2 TraesCS3D01G147900 chr3B 92.528 2021 67 34 104 2093 163657736 163659703 0.000000e+00 2819.0
3 TraesCS3D01G147900 chr3B 94.318 1760 60 14 2289 4035 163659864 163661596 0.000000e+00 2660.0
4 TraesCS3D01G147900 chr3B 97.368 38 1 0 1 38 163657554 163657591 9.360000e-07 65.8
5 TraesCS3D01G147900 chr3A 90.623 1845 92 31 281 2074 108372984 108374798 0.000000e+00 2374.0
6 TraesCS3D01G147900 chr3A 86.228 973 86 32 2286 3232 108375007 108375957 0.000000e+00 1011.0
7 TraesCS3D01G147900 chr3A 92.039 716 32 18 3323 4035 108376293 108376986 0.000000e+00 983.0
8 TraesCS3D01G147900 chr3A 91.111 90 8 0 30 119 492755963 492755874 5.480000e-24 122.0
9 TraesCS3D01G147900 chr5D 84.295 312 29 4 1909 2207 361591334 361591638 1.840000e-73 287.0
10 TraesCS3D01G147900 chr2D 83.974 312 30 6 1909 2207 129947608 129947912 8.540000e-72 281.0
11 TraesCS3D01G147900 chr1A 82.569 327 30 10 1909 2217 497218122 497218439 3.090000e-66 263.0
12 TraesCS3D01G147900 chr6A 95.294 85 4 0 31 115 613688331 613688247 7.030000e-28 135.0
13 TraesCS3D01G147900 chr6B 93.023 86 6 0 30 115 260182423 260182338 4.230000e-25 126.0
14 TraesCS3D01G147900 chr6B 93.023 86 6 0 30 115 531739478 531739563 4.230000e-25 126.0
15 TraesCS3D01G147900 chr6B 88.660 97 9 2 19 115 676145542 676145636 2.550000e-22 117.0
16 TraesCS3D01G147900 chr7A 91.209 91 8 0 31 121 589436528 589436618 1.520000e-24 124.0
17 TraesCS3D01G147900 chr4A 90.217 92 9 0 24 115 556378100 556378191 1.970000e-23 121.0
18 TraesCS3D01G147900 chr2B 88.542 96 11 0 24 119 394445651 394445746 2.550000e-22 117.0


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 TraesCS3D01G147900 chr3D 112690895 112694929 4034 False 7452.000000 7452 100.000 1 4035 1 chr3D.!!$F1 4034
1 TraesCS3D01G147900 chr3B 163657554 163661596 4042 False 1848.266667 2819 94.738 1 4035 3 chr3B.!!$F1 4034
2 TraesCS3D01G147900 chr3A 108372984 108376986 4002 False 1456.000000 2374 89.630 281 4035 3 chr3A.!!$F1 3754

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
444 537 2.434336 CTCGGAGAAGGAGAGAGAGAGA 59.566 54.545 0.00 0.00 34.09 3.10 F
1495 1643 0.458260 ACGGCGTCTGCATGTATACA 59.542 50.000 6.77 8.27 45.35 2.29 F
2018 2173 0.473755 TTGCCTCTGTTTGCTCCTCA 59.526 50.000 0.00 0.00 0.00 3.86 F
2530 2744 1.008538 CAGGCAAGTGAAACGCCAC 60.009 57.895 2.06 0.00 44.57 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1503 1651 0.317479 AAGTTTGAGACCTCGTCCCG 59.683 55.0 0.0 0.0 32.18 5.14 R
2919 3149 0.036732 ACTTCGCCAGCCAGAAATGA 59.963 50.0 0.0 0.0 0.00 2.57 R
2925 3155 0.037326 TACTTCACTTCGCCAGCCAG 60.037 55.0 0.0 0.0 0.00 4.85 R
3736 4272 0.533491 TTCGCTTGCAGGTATACGGT 59.467 50.0 0.0 0.0 0.00 4.83 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
39 40 2.752030 TGCTTAGCATGTACTCCCTCT 58.248 47.619 1.39 0.00 31.71 3.69
40 41 3.910989 TGCTTAGCATGTACTCCCTCTA 58.089 45.455 1.39 0.00 31.71 2.43
42 43 5.641155 TGCTTAGCATGTACTCCCTCTATA 58.359 41.667 1.39 0.00 31.71 1.31
43 44 6.075315 TGCTTAGCATGTACTCCCTCTATAA 58.925 40.000 1.39 0.00 31.71 0.98
44 45 6.553476 TGCTTAGCATGTACTCCCTCTATAAA 59.447 38.462 1.39 0.00 31.71 1.40
45 46 7.235606 TGCTTAGCATGTACTCCCTCTATAAAT 59.764 37.037 1.39 0.00 31.71 1.40
46 47 8.097662 GCTTAGCATGTACTCCCTCTATAAATT 58.902 37.037 0.00 0.00 0.00 1.82
120 200 7.775053 TTAGTTTACGGAGGGAGTAACTAAA 57.225 36.000 0.00 0.00 34.25 1.85
129 209 6.041751 CGGAGGGAGTAACTAAAATCATACCT 59.958 42.308 0.00 0.00 0.00 3.08
130 210 7.217906 GGAGGGAGTAACTAAAATCATACCTG 58.782 42.308 0.00 0.00 0.00 4.00
131 211 7.070821 GGAGGGAGTAACTAAAATCATACCTGA 59.929 40.741 0.00 0.00 35.41 3.86
132 212 8.568617 AGGGAGTAACTAAAATCATACCTGAT 57.431 34.615 0.00 0.00 44.14 2.90
133 213 9.670442 AGGGAGTAACTAAAATCATACCTGATA 57.330 33.333 0.00 0.00 41.34 2.15
156 236 5.509716 TTGATATAGACGTCGGTGTTGAT 57.490 39.130 10.46 0.00 0.00 2.57
159 239 5.240844 TGATATAGACGTCGGTGTTGATCAT 59.759 40.000 10.46 0.00 0.00 2.45
168 248 8.068893 ACGTCGGTGTTGATCATATAATTAAC 57.931 34.615 0.00 0.00 0.00 2.01
169 249 7.707464 ACGTCGGTGTTGATCATATAATTAACA 59.293 33.333 0.00 0.00 34.05 2.41
170 250 8.708742 CGTCGGTGTTGATCATATAATTAACAT 58.291 33.333 0.00 0.00 37.43 2.71
171 251 9.811655 GTCGGTGTTGATCATATAATTAACATG 57.188 33.333 0.00 0.00 37.43 3.21
172 252 9.554395 TCGGTGTTGATCATATAATTAACATGT 57.446 29.630 0.00 0.00 37.43 3.21
217 297 6.103997 TCAACGGGCGATTAATATCCTATTC 58.896 40.000 5.69 0.00 0.00 1.75
218 298 5.934402 ACGGGCGATTAATATCCTATTCT 57.066 39.130 5.69 0.00 0.00 2.40
219 299 7.123098 TCAACGGGCGATTAATATCCTATTCTA 59.877 37.037 5.69 0.00 0.00 2.10
444 537 2.434336 CTCGGAGAAGGAGAGAGAGAGA 59.566 54.545 0.00 0.00 34.09 3.10
451 544 4.653341 AGAAGGAGAGAGAGAGAGAGAGAG 59.347 50.000 0.00 0.00 0.00 3.20
453 546 4.222336 AGGAGAGAGAGAGAGAGAGAGAG 58.778 52.174 0.00 0.00 0.00 3.20
454 547 4.078922 AGGAGAGAGAGAGAGAGAGAGAGA 60.079 50.000 0.00 0.00 0.00 3.10
455 548 4.837860 GGAGAGAGAGAGAGAGAGAGAGAT 59.162 50.000 0.00 0.00 0.00 2.75
456 549 5.279406 GGAGAGAGAGAGAGAGAGAGAGATG 60.279 52.000 0.00 0.00 0.00 2.90
457 550 4.592351 AGAGAGAGAGAGAGAGAGAGATGG 59.408 50.000 0.00 0.00 0.00 3.51
458 551 4.560739 AGAGAGAGAGAGAGAGAGATGGA 58.439 47.826 0.00 0.00 0.00 3.41
459 552 4.592351 AGAGAGAGAGAGAGAGAGATGGAG 59.408 50.000 0.00 0.00 0.00 3.86
560 667 2.692709 TCATCTCATCTCCCTCCTCC 57.307 55.000 0.00 0.00 0.00 4.30
1304 1428 2.359107 CACGCTGCACCATCACCT 60.359 61.111 0.00 0.00 0.00 4.00
1492 1640 2.173669 GCACGGCGTCTGCATGTAT 61.174 57.895 10.85 0.00 45.35 2.29
1493 1641 0.874175 GCACGGCGTCTGCATGTATA 60.874 55.000 10.85 0.00 45.35 1.47
1494 1642 0.852777 CACGGCGTCTGCATGTATAC 59.147 55.000 10.85 0.00 45.35 1.47
1495 1643 0.458260 ACGGCGTCTGCATGTATACA 59.542 50.000 6.77 8.27 45.35 2.29
1496 1644 0.852777 CGGCGTCTGCATGTATACAC 59.147 55.000 7.96 0.00 45.35 2.90
1497 1645 0.852777 GGCGTCTGCATGTATACACG 59.147 55.000 7.96 7.30 45.35 4.49
1498 1646 0.852777 GCGTCTGCATGTATACACGG 59.147 55.000 7.96 4.86 42.15 4.94
1499 1647 1.535226 GCGTCTGCATGTATACACGGA 60.535 52.381 7.96 0.00 42.15 4.69
1500 1648 2.117137 CGTCTGCATGTATACACGGAC 58.883 52.381 18.84 18.84 0.00 4.79
1501 1649 2.117137 GTCTGCATGTATACACGGACG 58.883 52.381 15.73 2.82 0.00 4.79
1502 1650 2.018515 TCTGCATGTATACACGGACGA 58.981 47.619 7.96 0.00 0.00 4.20
1503 1651 2.117137 CTGCATGTATACACGGACGAC 58.883 52.381 7.96 0.00 0.00 4.34
1523 1671 2.545537 GGGACGAGGTCTCAAACTTT 57.454 50.000 0.00 0.00 32.50 2.66
1524 1672 2.143925 GGGACGAGGTCTCAAACTTTG 58.856 52.381 0.00 0.00 32.50 2.77
1525 1673 2.484947 GGGACGAGGTCTCAAACTTTGT 60.485 50.000 1.44 0.00 34.41 2.83
1537 1685 6.019559 GTCTCAAACTTTGTGCAAATCTTTCC 60.020 38.462 1.44 0.00 0.00 3.13
1538 1686 5.976458 TCAAACTTTGTGCAAATCTTTCCT 58.024 33.333 1.44 0.00 0.00 3.36
1539 1687 6.405538 TCAAACTTTGTGCAAATCTTTCCTT 58.594 32.000 1.44 0.00 0.00 3.36
1619 1767 4.549458 CCTTCAAACCAAATGTACAGCAG 58.451 43.478 0.33 0.00 0.00 4.24
1620 1768 3.641437 TCAAACCAAATGTACAGCAGC 57.359 42.857 0.33 0.00 0.00 5.25
1621 1769 2.954989 TCAAACCAAATGTACAGCAGCA 59.045 40.909 0.33 0.00 0.00 4.41
1622 1770 3.004629 TCAAACCAAATGTACAGCAGCAG 59.995 43.478 0.33 0.00 0.00 4.24
1623 1771 0.883833 ACCAAATGTACAGCAGCAGC 59.116 50.000 0.33 0.00 42.56 5.25
1624 1772 0.883153 CCAAATGTACAGCAGCAGCA 59.117 50.000 3.17 0.00 45.49 4.41
1625 1773 1.135489 CCAAATGTACAGCAGCAGCAG 60.135 52.381 3.17 0.00 45.49 4.24
1626 1774 0.524862 AAATGTACAGCAGCAGCAGC 59.475 50.000 3.17 0.46 45.49 5.25
1627 1775 0.607217 AATGTACAGCAGCAGCAGCA 60.607 50.000 12.92 0.00 45.49 4.41
1628 1776 1.025113 ATGTACAGCAGCAGCAGCAG 61.025 55.000 12.92 6.60 45.49 4.24
1702 1850 2.527100 GTATATATGTCTCACGCCGCC 58.473 52.381 0.00 0.00 0.00 6.13
1935 2089 2.095461 AGCAGATACGAGTTCAGAGCA 58.905 47.619 0.00 0.00 0.00 4.26
1974 2128 0.591170 TTGCAGTTTTAGCTCACCGC 59.409 50.000 0.00 0.00 39.57 5.68
2018 2173 0.473755 TTGCCTCTGTTTGCTCCTCA 59.526 50.000 0.00 0.00 0.00 3.86
2065 2223 9.019656 ACTGCATTGTTATTTACAGAATGGTAA 57.980 29.630 0.00 0.00 43.62 2.85
2086 2251 9.688091 TGGTAATAACTGTTATTTTATCCAGCA 57.312 29.630 25.68 19.47 37.12 4.41
2092 2257 8.863872 AACTGTTATTTTATCCAGCAGTTACT 57.136 30.769 0.00 0.00 41.84 2.24
2093 2258 8.268850 ACTGTTATTTTATCCAGCAGTTACTG 57.731 34.615 8.18 8.18 37.42 2.74
2104 2269 5.551760 CAGCAGTTACTGGTTCATTTAGG 57.448 43.478 14.81 0.00 40.40 2.69
2105 2270 5.003804 CAGCAGTTACTGGTTCATTTAGGT 58.996 41.667 14.81 0.00 40.40 3.08
2106 2271 6.170506 CAGCAGTTACTGGTTCATTTAGGTA 58.829 40.000 14.81 0.00 40.40 3.08
2107 2272 6.313905 CAGCAGTTACTGGTTCATTTAGGTAG 59.686 42.308 14.81 0.00 40.40 3.18
2108 2273 5.064834 GCAGTTACTGGTTCATTTAGGTAGC 59.935 44.000 14.63 0.00 31.21 3.58
2109 2274 6.170506 CAGTTACTGGTTCATTTAGGTAGCA 58.829 40.000 4.14 0.00 0.00 3.49
2110 2275 6.313905 CAGTTACTGGTTCATTTAGGTAGCAG 59.686 42.308 4.14 0.00 40.81 4.24
2111 2276 4.222124 ACTGGTTCATTTAGGTAGCAGG 57.778 45.455 0.00 0.00 39.68 4.85
2112 2277 3.844211 ACTGGTTCATTTAGGTAGCAGGA 59.156 43.478 0.00 0.00 39.68 3.86
2113 2278 4.288626 ACTGGTTCATTTAGGTAGCAGGAA 59.711 41.667 0.00 0.00 39.68 3.36
2114 2279 5.222048 ACTGGTTCATTTAGGTAGCAGGAAA 60.222 40.000 0.00 0.00 39.68 3.13
2115 2280 5.826643 TGGTTCATTTAGGTAGCAGGAAAT 58.173 37.500 0.00 0.00 0.00 2.17
2116 2281 6.252995 TGGTTCATTTAGGTAGCAGGAAATT 58.747 36.000 0.00 0.00 0.00 1.82
2117 2282 7.406916 TGGTTCATTTAGGTAGCAGGAAATTA 58.593 34.615 0.00 0.00 0.00 1.40
2118 2283 8.058847 TGGTTCATTTAGGTAGCAGGAAATTAT 58.941 33.333 0.00 0.00 0.00 1.28
2119 2284 9.569122 GGTTCATTTAGGTAGCAGGAAATTATA 57.431 33.333 0.00 0.00 0.00 0.98
2125 2290 9.793259 TTTAGGTAGCAGGAAATTATATTGGAG 57.207 33.333 0.00 0.00 0.00 3.86
2126 2291 7.633018 AGGTAGCAGGAAATTATATTGGAGA 57.367 36.000 0.00 0.00 0.00 3.71
2127 2292 8.045720 AGGTAGCAGGAAATTATATTGGAGAA 57.954 34.615 0.00 0.00 0.00 2.87
2128 2293 7.939588 AGGTAGCAGGAAATTATATTGGAGAAC 59.060 37.037 0.00 0.00 0.00 3.01
2129 2294 7.719633 GGTAGCAGGAAATTATATTGGAGAACA 59.280 37.037 0.00 0.00 0.00 3.18
2130 2295 9.289782 GTAGCAGGAAATTATATTGGAGAACAT 57.710 33.333 0.00 0.00 0.00 2.71
2131 2296 8.174733 AGCAGGAAATTATATTGGAGAACATG 57.825 34.615 0.00 0.00 0.00 3.21
2132 2297 7.781693 AGCAGGAAATTATATTGGAGAACATGT 59.218 33.333 0.00 0.00 0.00 3.21
2133 2298 8.078596 GCAGGAAATTATATTGGAGAACATGTC 58.921 37.037 0.00 0.00 0.00 3.06
2134 2299 9.123902 CAGGAAATTATATTGGAGAACATGTCA 57.876 33.333 0.00 0.00 0.00 3.58
2152 2317 6.994496 ACATGTCACATTTACTCCTATCCATG 59.006 38.462 0.00 0.00 0.00 3.66
2164 2330 5.169992 TCCTATCCATGCCAATATCACTG 57.830 43.478 0.00 0.00 0.00 3.66
2200 2368 3.128589 CACCCCGTTGAATTTACCTGATG 59.871 47.826 0.00 0.00 0.00 3.07
2208 2376 6.306356 CGTTGAATTTACCTGATGAAAAGCTG 59.694 38.462 0.00 0.00 0.00 4.24
2215 2383 4.464008 ACCTGATGAAAAGCTGAGAAACA 58.536 39.130 0.00 0.00 0.00 2.83
2220 2388 7.137490 TGATGAAAAGCTGAGAAACACATAG 57.863 36.000 0.00 0.00 0.00 2.23
2222 2390 4.216257 TGAAAAGCTGAGAAACACATAGCC 59.784 41.667 0.00 0.00 35.05 3.93
2229 2397 6.072452 AGCTGAGAAACACATAGCCTTTTTAC 60.072 38.462 0.00 0.00 35.05 2.01
2310 2518 2.957402 TTCACCTTTCATCTGTGCCT 57.043 45.000 0.00 0.00 0.00 4.75
2485 2699 4.124351 CGGAGTACGGCGGCTTCA 62.124 66.667 13.24 0.00 39.42 3.02
2486 2700 2.202756 GGAGTACGGCGGCTTCAG 60.203 66.667 13.24 0.00 0.00 3.02
2487 2701 2.572284 GAGTACGGCGGCTTCAGT 59.428 61.111 13.24 0.00 0.00 3.41
2488 2702 1.805945 GAGTACGGCGGCTTCAGTG 60.806 63.158 13.24 0.00 0.00 3.66
2489 2703 3.488090 GTACGGCGGCTTCAGTGC 61.488 66.667 13.24 0.00 0.00 4.40
2530 2744 1.008538 CAGGCAAGTGAAACGCCAC 60.009 57.895 2.06 0.00 44.57 5.01
2550 2764 2.367567 ACGCTCTTCTGAACCCTGTAAA 59.632 45.455 0.00 0.00 0.00 2.01
2555 2769 5.703876 CTCTTCTGAACCCTGTAAAAATGC 58.296 41.667 0.00 0.00 0.00 3.56
2586 2800 5.233225 TGCTCTGACTGTAACTGATGAAAG 58.767 41.667 0.00 0.00 0.00 2.62
2590 2804 5.928839 TCTGACTGTAACTGATGAAAGCTTC 59.071 40.000 0.00 0.00 0.00 3.86
2886 3103 6.478512 TTTTCACTGCCAATAAACCTTCTT 57.521 33.333 0.00 0.00 0.00 2.52
2914 3144 3.850122 GGTTCAATTTACTGAGCCACC 57.150 47.619 2.03 0.00 43.99 4.61
2915 3145 3.153919 GGTTCAATTTACTGAGCCACCA 58.846 45.455 2.03 0.00 43.99 4.17
2916 3146 3.763897 GGTTCAATTTACTGAGCCACCAT 59.236 43.478 2.03 0.00 43.99 3.55
2917 3147 4.380867 GGTTCAATTTACTGAGCCACCATG 60.381 45.833 2.03 0.00 43.99 3.66
2918 3148 4.032960 TCAATTTACTGAGCCACCATGT 57.967 40.909 0.00 0.00 0.00 3.21
2919 3149 4.406456 TCAATTTACTGAGCCACCATGTT 58.594 39.130 0.00 0.00 0.00 2.71
2920 3150 4.458989 TCAATTTACTGAGCCACCATGTTC 59.541 41.667 0.00 0.00 0.00 3.18
2921 3151 3.500448 TTTACTGAGCCACCATGTTCA 57.500 42.857 0.00 0.00 0.00 3.18
2922 3152 3.719268 TTACTGAGCCACCATGTTCAT 57.281 42.857 0.00 0.00 0.00 2.57
2923 3153 2.592102 ACTGAGCCACCATGTTCATT 57.408 45.000 0.00 0.00 0.00 2.57
2924 3154 2.880443 ACTGAGCCACCATGTTCATTT 58.120 42.857 0.00 0.00 0.00 2.32
2925 3155 2.821969 ACTGAGCCACCATGTTCATTTC 59.178 45.455 0.00 0.00 0.00 2.17
2926 3156 3.087031 CTGAGCCACCATGTTCATTTCT 58.913 45.455 0.00 0.00 0.00 2.52
2927 3157 2.821378 TGAGCCACCATGTTCATTTCTG 59.179 45.455 0.00 0.00 0.00 3.02
2928 3158 2.165030 GAGCCACCATGTTCATTTCTGG 59.835 50.000 0.00 0.00 34.84 3.86
2971 3204 2.825836 GCATGACGGAAGCAGGGG 60.826 66.667 0.00 0.00 0.00 4.79
3096 3329 1.105167 ATCGTGCAAGGATGGGCATG 61.105 55.000 0.00 0.00 45.94 4.06
3214 3468 4.631131 TGCCACTCCATAATCTTCATACG 58.369 43.478 0.00 0.00 0.00 3.06
3288 3822 0.112606 TAGCTCCCAGTATCCTCCGG 59.887 60.000 0.00 0.00 0.00 5.14
3295 3830 3.173965 CCCAGTATCCTCCGGATATGTT 58.826 50.000 3.57 0.00 45.08 2.71
3301 3836 7.980099 CCAGTATCCTCCGGATATGTTTAATAC 59.020 40.741 3.57 4.83 45.08 1.89
3306 3841 6.271391 TCCTCCGGATATGTTTAATACACCAT 59.729 38.462 3.57 0.00 40.19 3.55
3330 3865 3.132289 ACCGAAGAGAAGAGAACACACAA 59.868 43.478 0.00 0.00 0.00 3.33
3413 3949 6.601613 TGGATATGAACACAATAAACACCTCC 59.398 38.462 0.00 0.00 0.00 4.30
3458 3994 3.138304 TGAGTCAAAAATCACGACAGGG 58.862 45.455 0.00 0.00 31.92 4.45
3655 4191 1.511305 GATGACGAGCACCTCCGAA 59.489 57.895 0.00 0.00 0.00 4.30
3709 4245 2.281484 GCCAAGAACACGCCCAGA 60.281 61.111 0.00 0.00 0.00 3.86
3715 4251 2.591715 AACACGCCCAGACACAGC 60.592 61.111 0.00 0.00 0.00 4.40
3803 4339 5.502079 TGTTCTTAGTCCAGAGTAGAGAGG 58.498 45.833 0.00 0.00 0.00 3.69
3804 4340 4.159244 TCTTAGTCCAGAGTAGAGAGGC 57.841 50.000 0.00 0.00 0.00 4.70
3811 4347 1.451747 GAGTAGAGAGGCGGACGGT 60.452 63.158 0.00 0.00 0.00 4.83
3812 4348 1.001145 AGTAGAGAGGCGGACGGTT 60.001 57.895 0.00 0.00 0.00 4.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 0.239347 GCTAAGCATATTGGCCGCTG 59.761 55.000 2.61 0.00 35.79 5.18
85 86 8.761689 TCCCTCCGTAAACTAATATAAAAGTGT 58.238 33.333 0.00 0.00 0.00 3.55
86 87 9.257651 CTCCCTCCGTAAACTAATATAAAAGTG 57.742 37.037 0.00 0.00 0.00 3.16
87 88 8.985922 ACTCCCTCCGTAAACTAATATAAAAGT 58.014 33.333 0.00 0.00 0.00 2.66
93 94 9.646522 TTAGTTACTCCCTCCGTAAACTAATAT 57.353 33.333 0.00 0.00 0.00 1.28
94 95 9.474313 TTTAGTTACTCCCTCCGTAAACTAATA 57.526 33.333 6.37 0.00 30.32 0.98
95 96 7.961326 TTAGTTACTCCCTCCGTAAACTAAT 57.039 36.000 0.00 0.00 0.00 1.73
96 97 7.775053 TTTAGTTACTCCCTCCGTAAACTAA 57.225 36.000 0.00 0.00 0.00 2.24
100 101 7.243604 TGATTTTAGTTACTCCCTCCGTAAA 57.756 36.000 0.00 0.00 0.00 2.01
101 102 6.855763 TGATTTTAGTTACTCCCTCCGTAA 57.144 37.500 0.00 0.00 0.00 3.18
102 103 7.014615 GGTATGATTTTAGTTACTCCCTCCGTA 59.985 40.741 0.00 0.00 0.00 4.02
129 209 6.812879 ACACCGACGTCTATATCAATATCA 57.187 37.500 14.70 0.00 0.00 2.15
130 210 7.303261 TCAACACCGACGTCTATATCAATATC 58.697 38.462 14.70 0.00 0.00 1.63
131 211 7.210718 TCAACACCGACGTCTATATCAATAT 57.789 36.000 14.70 0.00 0.00 1.28
132 212 6.622833 TCAACACCGACGTCTATATCAATA 57.377 37.500 14.70 0.00 0.00 1.90
133 213 5.509716 TCAACACCGACGTCTATATCAAT 57.490 39.130 14.70 0.00 0.00 2.57
134 214 4.968812 TCAACACCGACGTCTATATCAA 57.031 40.909 14.70 0.00 0.00 2.57
175 255 7.975616 GCCCGTTGATATTACGTAGGATATTAA 59.024 37.037 0.00 0.00 37.30 1.40
176 256 7.483307 GCCCGTTGATATTACGTAGGATATTA 58.517 38.462 0.00 0.00 37.30 0.98
177 257 6.335777 GCCCGTTGATATTACGTAGGATATT 58.664 40.000 0.00 0.00 37.30 1.28
178 258 5.449588 CGCCCGTTGATATTACGTAGGATAT 60.450 44.000 0.00 0.00 37.30 1.63
183 263 3.272439 TCGCCCGTTGATATTACGTAG 57.728 47.619 0.00 3.64 37.30 3.51
187 267 7.709613 AGGATATTAATCGCCCGTTGATATTAC 59.290 37.037 0.00 0.00 32.44 1.89
252 341 2.301870 TCCGCTTAACTCTCCACAACAT 59.698 45.455 0.00 0.00 0.00 2.71
444 537 1.815408 GCTCGCTCCATCTCTCTCTCT 60.815 57.143 0.00 0.00 0.00 3.10
451 544 0.108424 ACACAAGCTCGCTCCATCTC 60.108 55.000 0.00 0.00 0.00 2.75
453 546 0.671781 ACACACAAGCTCGCTCCATC 60.672 55.000 0.00 0.00 0.00 3.51
454 547 0.671781 GACACACAAGCTCGCTCCAT 60.672 55.000 0.00 0.00 0.00 3.41
455 548 1.300931 GACACACAAGCTCGCTCCA 60.301 57.895 0.00 0.00 0.00 3.86
456 549 0.671781 ATGACACACAAGCTCGCTCC 60.672 55.000 0.00 0.00 0.00 4.70
457 550 0.441533 CATGACACACAAGCTCGCTC 59.558 55.000 0.00 0.00 0.00 5.03
458 551 0.250038 ACATGACACACAAGCTCGCT 60.250 50.000 0.00 0.00 0.00 4.93
459 552 0.164647 GACATGACACACAAGCTCGC 59.835 55.000 0.00 0.00 0.00 5.03
515 608 6.488683 TGGGATCGTATCTTGTTTCTTTTTGT 59.511 34.615 0.00 0.00 0.00 2.83
560 667 2.285083 CTCACTAGACACGGAGAGAGG 58.715 57.143 0.00 0.00 29.68 3.69
885 1006 2.272146 GCATCACGGACCCATGGT 59.728 61.111 11.73 0.00 39.44 3.55
1074 1198 4.973360 CCGTTGCCGTTGCCGTTG 62.973 66.667 0.00 0.00 36.33 4.10
1428 1555 0.323725 CCATTGGGAGTGGAGGTTGG 60.324 60.000 0.00 0.00 39.12 3.77
1483 1631 2.117137 GTCGTCCGTGTATACATGCAG 58.883 52.381 18.08 11.51 0.00 4.41
1492 1640 3.422303 CGTCCCGTCGTCCGTGTA 61.422 66.667 0.00 0.00 33.66 2.90
1494 1642 4.456253 CTCGTCCCGTCGTCCGTG 62.456 72.222 0.00 0.00 33.66 4.94
1497 1645 3.808656 GACCTCGTCCCGTCGTCC 61.809 72.222 0.00 0.00 0.00 4.79
1498 1646 2.745492 AGACCTCGTCCCGTCGTC 60.745 66.667 0.00 0.00 34.10 4.20
1499 1647 2.745492 GAGACCTCGTCCCGTCGT 60.745 66.667 0.00 0.00 34.10 4.34
1500 1648 1.859427 TTTGAGACCTCGTCCCGTCG 61.859 60.000 0.00 0.00 34.10 5.12
1501 1649 0.388263 GTTTGAGACCTCGTCCCGTC 60.388 60.000 0.00 0.00 32.18 4.79
1502 1650 0.826672 AGTTTGAGACCTCGTCCCGT 60.827 55.000 0.00 0.00 32.18 5.28
1503 1651 0.317479 AAGTTTGAGACCTCGTCCCG 59.683 55.000 0.00 0.00 32.18 5.14
1504 1652 2.143925 CAAAGTTTGAGACCTCGTCCC 58.856 52.381 10.19 0.00 32.18 4.46
1506 1654 2.032808 GCACAAAGTTTGAGACCTCGTC 60.033 50.000 22.23 0.00 0.00 4.20
1523 1671 3.295093 TGGTCAAGGAAAGATTTGCACA 58.705 40.909 0.00 0.00 0.00 4.57
1524 1672 3.905784 CTGGTCAAGGAAAGATTTGCAC 58.094 45.455 0.00 0.00 0.00 4.57
1537 1685 1.669115 CCGTGCTCACCTGGTCAAG 60.669 63.158 0.00 0.00 0.00 3.02
1538 1686 2.425592 CCGTGCTCACCTGGTCAA 59.574 61.111 0.00 0.00 0.00 3.18
1539 1687 3.625897 CCCGTGCTCACCTGGTCA 61.626 66.667 0.00 0.00 0.00 4.02
1620 1768 3.128188 CTCCTGCTGCTGCTGCTG 61.128 66.667 27.67 25.97 40.48 4.41
1621 1769 4.411981 CCTCCTGCTGCTGCTGCT 62.412 66.667 27.67 0.00 40.48 4.24
1622 1770 4.405671 TCCTCCTGCTGCTGCTGC 62.406 66.667 22.51 22.51 40.48 5.25
1623 1771 2.125065 CTCCTCCTGCTGCTGCTG 60.125 66.667 17.00 15.58 40.48 4.41
1624 1772 4.098722 GCTCCTCCTGCTGCTGCT 62.099 66.667 17.00 0.00 40.48 4.24
1625 1773 4.405671 TGCTCCTCCTGCTGCTGC 62.406 66.667 8.89 8.89 40.20 5.25
1626 1774 2.125065 CTGCTCCTCCTGCTGCTG 60.125 66.667 0.00 0.00 0.00 4.41
1627 1775 4.098722 GCTGCTCCTCCTGCTGCT 62.099 66.667 0.00 0.00 46.79 4.24
1702 1850 1.002134 AGGCAAGTTCATCACGGGG 60.002 57.895 0.00 0.00 0.00 5.73
1935 2089 7.397192 ACTGCAATCTACCTGAAATAATTGGTT 59.603 33.333 0.00 0.00 34.33 3.67
1984 2139 5.985530 ACAGAGGCAAGAATTTAAACTTTGC 59.014 36.000 17.97 17.97 0.00 3.68
2018 2173 5.299279 CAGTGAAATTACTTGCCCGGAATAT 59.701 40.000 0.73 0.00 0.00 1.28
2085 2250 6.170506 TGCTACCTAAATGAACCAGTAACTG 58.829 40.000 0.00 0.00 0.00 3.16
2086 2251 6.368779 TGCTACCTAAATGAACCAGTAACT 57.631 37.500 0.00 0.00 0.00 2.24
2087 2252 5.585047 CCTGCTACCTAAATGAACCAGTAAC 59.415 44.000 0.00 0.00 0.00 2.50
2088 2253 5.486063 TCCTGCTACCTAAATGAACCAGTAA 59.514 40.000 0.00 0.00 0.00 2.24
2089 2254 5.027460 TCCTGCTACCTAAATGAACCAGTA 58.973 41.667 0.00 0.00 0.00 2.74
2090 2255 3.844211 TCCTGCTACCTAAATGAACCAGT 59.156 43.478 0.00 0.00 0.00 4.00
2091 2256 4.487714 TCCTGCTACCTAAATGAACCAG 57.512 45.455 0.00 0.00 0.00 4.00
2092 2257 4.919774 TTCCTGCTACCTAAATGAACCA 57.080 40.909 0.00 0.00 0.00 3.67
2093 2258 6.775594 AATTTCCTGCTACCTAAATGAACC 57.224 37.500 0.00 0.00 0.00 3.62
2099 2264 9.793259 CTCCAATATAATTTCCTGCTACCTAAA 57.207 33.333 0.00 0.00 0.00 1.85
2100 2265 9.166222 TCTCCAATATAATTTCCTGCTACCTAA 57.834 33.333 0.00 0.00 0.00 2.69
2101 2266 8.736097 TCTCCAATATAATTTCCTGCTACCTA 57.264 34.615 0.00 0.00 0.00 3.08
2102 2267 7.633018 TCTCCAATATAATTTCCTGCTACCT 57.367 36.000 0.00 0.00 0.00 3.08
2103 2268 7.719633 TGTTCTCCAATATAATTTCCTGCTACC 59.280 37.037 0.00 0.00 0.00 3.18
2104 2269 8.677148 TGTTCTCCAATATAATTTCCTGCTAC 57.323 34.615 0.00 0.00 0.00 3.58
2105 2270 9.288576 CATGTTCTCCAATATAATTTCCTGCTA 57.711 33.333 0.00 0.00 0.00 3.49
2106 2271 7.781693 ACATGTTCTCCAATATAATTTCCTGCT 59.218 33.333 0.00 0.00 0.00 4.24
2107 2272 7.945134 ACATGTTCTCCAATATAATTTCCTGC 58.055 34.615 0.00 0.00 0.00 4.85
2108 2273 9.123902 TGACATGTTCTCCAATATAATTTCCTG 57.876 33.333 0.00 0.00 0.00 3.86
2109 2274 9.125026 GTGACATGTTCTCCAATATAATTTCCT 57.875 33.333 0.00 0.00 0.00 3.36
2110 2275 8.902806 TGTGACATGTTCTCCAATATAATTTCC 58.097 33.333 0.00 0.00 0.00 3.13
2117 2282 9.113838 GAGTAAATGTGACATGTTCTCCAATAT 57.886 33.333 10.32 0.00 0.00 1.28
2118 2283 7.552687 GGAGTAAATGTGACATGTTCTCCAATA 59.447 37.037 27.04 0.00 38.81 1.90
2119 2284 6.375455 GGAGTAAATGTGACATGTTCTCCAAT 59.625 38.462 27.04 0.00 38.81 3.16
2120 2285 5.705441 GGAGTAAATGTGACATGTTCTCCAA 59.295 40.000 27.04 0.00 38.81 3.53
2121 2286 5.013079 AGGAGTAAATGTGACATGTTCTCCA 59.987 40.000 30.86 0.00 40.65 3.86
2122 2287 5.491982 AGGAGTAAATGTGACATGTTCTCC 58.508 41.667 25.55 25.55 39.12 3.71
2123 2288 7.439655 GGATAGGAGTAAATGTGACATGTTCTC 59.560 40.741 12.42 12.42 0.00 2.87
2124 2289 7.092891 TGGATAGGAGTAAATGTGACATGTTCT 60.093 37.037 0.00 0.00 0.00 3.01
2125 2290 7.047891 TGGATAGGAGTAAATGTGACATGTTC 58.952 38.462 0.00 0.00 0.00 3.18
2126 2291 6.957631 TGGATAGGAGTAAATGTGACATGTT 58.042 36.000 0.00 0.00 0.00 2.71
2127 2292 6.560003 TGGATAGGAGTAAATGTGACATGT 57.440 37.500 0.00 0.00 0.00 3.21
2128 2293 6.072838 GCATGGATAGGAGTAAATGTGACATG 60.073 42.308 0.00 0.00 35.28 3.21
2129 2294 6.000219 GCATGGATAGGAGTAAATGTGACAT 59.000 40.000 0.00 0.00 0.00 3.06
2130 2295 5.368145 GCATGGATAGGAGTAAATGTGACA 58.632 41.667 0.00 0.00 0.00 3.58
2131 2296 4.757149 GGCATGGATAGGAGTAAATGTGAC 59.243 45.833 0.00 0.00 0.00 3.67
2132 2297 4.411869 TGGCATGGATAGGAGTAAATGTGA 59.588 41.667 0.00 0.00 0.00 3.58
2133 2298 4.717877 TGGCATGGATAGGAGTAAATGTG 58.282 43.478 0.00 0.00 0.00 3.21
2134 2299 5.387113 TTGGCATGGATAGGAGTAAATGT 57.613 39.130 0.00 0.00 0.00 2.71
2137 2302 7.017551 AGTGATATTGGCATGGATAGGAGTAAA 59.982 37.037 0.00 0.00 0.00 2.01
2152 2317 6.799512 AGCTGTAAATTTCAGTGATATTGGC 58.200 36.000 9.25 10.77 35.60 4.52
2164 2330 2.817844 ACGGGGTGAAGCTGTAAATTTC 59.182 45.455 0.00 0.00 0.00 2.17
2200 2368 4.457257 AGGCTATGTGTTTCTCAGCTTTTC 59.543 41.667 0.00 0.00 32.78 2.29
2208 2376 6.569179 TGGTAAAAAGGCTATGTGTTTCTC 57.431 37.500 0.00 0.00 0.00 2.87
2220 2388 9.369904 CATGGCAAATATATATGGTAAAAAGGC 57.630 33.333 0.00 0.00 0.00 4.35
2288 2496 3.960102 AGGCACAGATGAAAGGTGAAAAA 59.040 39.130 0.00 0.00 34.52 1.94
2293 2501 1.068055 GCAAGGCACAGATGAAAGGTG 60.068 52.381 0.00 0.00 35.68 4.00
2294 2502 1.251251 GCAAGGCACAGATGAAAGGT 58.749 50.000 0.00 0.00 0.00 3.50
2295 2503 1.201647 CTGCAAGGCACAGATGAAAGG 59.798 52.381 0.00 0.00 37.32 3.11
2297 2505 1.610038 CACTGCAAGGCACAGATGAAA 59.390 47.619 8.87 0.00 39.30 2.69
2310 2518 1.646540 GTACGCACTTGCACTGCAA 59.353 52.632 15.63 15.63 46.80 4.08
2480 2694 2.595463 TGGCACTGGCACTGAAGC 60.595 61.111 0.07 0.00 43.71 3.86
2530 2744 2.743636 TTACAGGGTTCAGAAGAGCG 57.256 50.000 0.00 0.00 0.00 5.03
2550 2764 0.520404 CAGAGCAAGCTCACGCATTT 59.480 50.000 22.68 0.00 44.99 2.32
2555 2769 0.319383 ACAGTCAGAGCAAGCTCACG 60.319 55.000 22.68 13.67 44.99 4.35
2586 2800 0.176680 TCCCGAGCTGATCAAGAAGC 59.823 55.000 0.00 0.00 39.82 3.86
2675 2889 3.222855 CGCTCGGGGCTCTCTCAT 61.223 66.667 0.00 0.00 39.13 2.90
2886 3103 6.318648 GGCTCAGTAAATTGAACCATATCACA 59.681 38.462 0.00 0.00 34.24 3.58
2913 3143 1.134907 GCCAGCCAGAAATGAACATGG 60.135 52.381 0.00 0.00 35.84 3.66
2914 3144 1.468565 CGCCAGCCAGAAATGAACATG 60.469 52.381 0.00 0.00 0.00 3.21
2915 3145 0.813184 CGCCAGCCAGAAATGAACAT 59.187 50.000 0.00 0.00 0.00 2.71
2916 3146 0.250684 TCGCCAGCCAGAAATGAACA 60.251 50.000 0.00 0.00 0.00 3.18
2917 3147 0.881118 TTCGCCAGCCAGAAATGAAC 59.119 50.000 0.00 0.00 0.00 3.18
2918 3148 1.167851 CTTCGCCAGCCAGAAATGAA 58.832 50.000 0.00 0.00 0.00 2.57
2919 3149 0.036732 ACTTCGCCAGCCAGAAATGA 59.963 50.000 0.00 0.00 0.00 2.57
2920 3150 0.169672 CACTTCGCCAGCCAGAAATG 59.830 55.000 0.00 0.00 0.00 2.32
2921 3151 0.036732 TCACTTCGCCAGCCAGAAAT 59.963 50.000 0.00 0.00 0.00 2.17
2922 3152 0.179032 TTCACTTCGCCAGCCAGAAA 60.179 50.000 0.00 0.00 0.00 2.52
2923 3153 0.603707 CTTCACTTCGCCAGCCAGAA 60.604 55.000 0.00 0.00 0.00 3.02
2924 3154 1.004560 CTTCACTTCGCCAGCCAGA 60.005 57.895 0.00 0.00 0.00 3.86
2925 3155 0.037326 TACTTCACTTCGCCAGCCAG 60.037 55.000 0.00 0.00 0.00 4.85
2926 3156 0.037326 CTACTTCACTTCGCCAGCCA 60.037 55.000 0.00 0.00 0.00 4.75
2927 3157 0.246635 TCTACTTCACTTCGCCAGCC 59.753 55.000 0.00 0.00 0.00 4.85
2928 3158 1.634702 CTCTACTTCACTTCGCCAGC 58.365 55.000 0.00 0.00 0.00 4.85
2971 3204 2.623416 GCCTGGACCATACATAAAAGCC 59.377 50.000 0.00 0.00 0.00 4.35
3096 3329 0.801251 CACAAGCTAGCTGTGAAGCC 59.199 55.000 28.62 0.00 39.64 4.35
3144 3381 5.159209 GTGAGAGAGAAAATTGCATTGTGG 58.841 41.667 0.00 0.00 0.00 4.17
3214 3468 7.069950 ACCTATTTTATCTGGATTTTGCCCTTC 59.930 37.037 0.00 0.00 0.00 3.46
3245 3779 9.270640 CTACATGCTAGAAATAAGCTTGAGATT 57.729 33.333 9.86 0.00 43.94 2.40
3246 3780 7.387397 GCTACATGCTAGAAATAAGCTTGAGAT 59.613 37.037 9.86 0.00 43.94 2.75
3247 3781 6.703607 GCTACATGCTAGAAATAAGCTTGAGA 59.296 38.462 9.86 0.00 43.94 3.27
3248 3782 6.886307 GCTACATGCTAGAAATAAGCTTGAG 58.114 40.000 9.86 10.15 43.94 3.02
3249 3783 6.851222 GCTACATGCTAGAAATAAGCTTGA 57.149 37.500 9.86 0.00 43.94 3.02
3295 3830 8.070034 TCTTCTCTTCGGTAATGGTGTATTAA 57.930 34.615 0.00 0.00 33.22 1.40
3301 3836 4.720649 TCTCTTCTCTTCGGTAATGGTG 57.279 45.455 0.00 0.00 0.00 4.17
3306 3841 4.340097 TGTGTGTTCTCTTCTCTTCGGTAA 59.660 41.667 0.00 0.00 0.00 2.85
3458 3994 1.003866 GGACACACGCTTGAGTTTGAC 60.004 52.381 0.00 0.00 0.00 3.18
3655 4191 0.540830 AGCTGACGTGGGACTTCTCT 60.541 55.000 0.00 0.00 0.00 3.10
3715 4251 1.002900 GGTGTGACCATGAACAACACG 60.003 52.381 0.00 0.00 38.42 4.49
3736 4272 0.533491 TTCGCTTGCAGGTATACGGT 59.467 50.000 0.00 0.00 0.00 4.83
3803 4339 1.431496 TAGCTTGTAAAACCGTCCGC 58.569 50.000 0.00 0.00 0.00 5.54
3804 4340 2.414138 CCTTAGCTTGTAAAACCGTCCG 59.586 50.000 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.