Multiple sequence alignment - TraesCS3D01G189900

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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 TraesCS3D01G189900 chr3D 100.000 3835 0 0 1 3835 177776865 177780699 0.000000e+00 7083.0
1 TraesCS3D01G189900 chr3D 95.556 90 4 0 1393 1482 476327007 476326918 1.110000e-30 145.0
2 TraesCS3D01G189900 chr3D 84.615 104 16 0 2156 2259 95840039 95839936 1.880000e-18 104.0
3 TraesCS3D01G189900 chr3B 94.858 2178 60 20 961 3122 256433425 256435566 0.000000e+00 3354.0
4 TraesCS3D01G189900 chr3B 90.554 614 39 6 3120 3716 256450336 256450947 0.000000e+00 795.0
5 TraesCS3D01G189900 chr3B 89.140 442 20 9 528 960 256432657 256433079 3.390000e-145 525.0
6 TraesCS3D01G189900 chr3B 85.965 513 27 15 1 493 256432083 256432570 1.230000e-139 507.0
7 TraesCS3D01G189900 chr3B 84.615 104 16 0 2156 2259 146706719 146706616 1.880000e-18 104.0
8 TraesCS3D01G189900 chr3A 92.106 2217 98 27 1662 3835 218728917 218731099 0.000000e+00 3053.0
9 TraesCS3D01G189900 chr3A 91.975 1134 38 25 528 1632 218727810 218728919 0.000000e+00 1541.0
10 TraesCS3D01G189900 chr3A 89.971 349 23 4 159 500 218727388 218727731 1.260000e-119 440.0
11 TraesCS3D01G189900 chr3A 95.833 144 6 0 1 144 218726218 218726361 2.300000e-57 233.0
12 TraesCS3D01G189900 chr3A 90.678 118 8 3 3721 3835 317388014 317388131 1.840000e-33 154.0
13 TraesCS3D01G189900 chr3A 85.577 104 15 0 2156 2259 113922179 113922076 4.050000e-20 110.0
14 TraesCS3D01G189900 chr6A 96.939 98 3 0 3738 3835 246500941 246501038 8.520000e-37 165.0
15 TraesCS3D01G189900 chr1D 96.939 98 3 0 3738 3835 146170717 146170620 8.520000e-37 165.0
16 TraesCS3D01G189900 chr1D 90.476 42 2 1 1225 1266 288539996 288540035 2.000000e-03 54.7
17 TraesCS3D01G189900 chr7A 93.636 110 3 3 3726 3833 441624421 441624528 1.100000e-35 161.0
18 TraesCS3D01G189900 chr7A 79.562 137 21 6 2123 2254 670946874 670946740 1.470000e-14 91.6
19 TraesCS3D01G189900 chr1A 92.035 113 8 1 3724 3835 343884678 343884790 1.430000e-34 158.0
20 TraesCS3D01G189900 chr1A 92.105 38 3 0 1235 1272 359981297 359981260 2.000000e-03 54.7
21 TraesCS3D01G189900 chr1B 91.892 111 9 0 3725 3835 148962150 148962040 5.130000e-34 156.0
22 TraesCS3D01G189900 chr1B 94.444 36 2 0 1231 1266 389942941 389942976 5.350000e-04 56.5
23 TraesCS3D01G189900 chr5D 94.845 97 5 0 3739 3835 496166096 496166000 6.640000e-33 152.0
24 TraesCS3D01G189900 chr4D 91.228 114 6 4 3724 3835 235387032 235386921 6.640000e-33 152.0
25 TraesCS3D01G189900 chr2A 90.598 117 7 4 3722 3835 501400584 501400699 6.640000e-33 152.0
26 TraesCS3D01G189900 chr2A 92.727 55 4 0 2405 2459 262118020 262117966 3.180000e-11 80.5
27 TraesCS3D01G189900 chr2A 92.453 53 4 0 2412 2464 768627141 768627193 4.110000e-10 76.8
28 TraesCS3D01G189900 chr2A 89.831 59 4 2 2406 2463 700976373 700976430 1.480000e-09 75.0
29 TraesCS3D01G189900 chr2A 94.286 35 2 0 1232 1266 58824670 58824704 2.000000e-03 54.7
30 TraesCS3D01G189900 chr2D 87.368 95 9 3 2166 2259 95645152 95645244 5.240000e-19 106.0
31 TraesCS3D01G189900 chr2D 89.552 67 7 0 2393 2459 209025376 209025310 6.830000e-13 86.1
32 TraesCS3D01G189900 chr2D 89.831 59 4 2 2406 2463 560992417 560992474 1.480000e-09 75.0
33 TraesCS3D01G189900 chr2D 94.444 36 2 0 1231 1266 59627177 59627212 5.350000e-04 56.5
34 TraesCS3D01G189900 chr2B 86.316 95 10 3 2166 2259 146992941 146993033 2.440000e-17 100.0
35 TraesCS3D01G189900 chr2B 92.727 55 4 0 2405 2459 263812031 263811977 3.180000e-11 80.5
36 TraesCS3D01G189900 chr2B 90.909 55 3 2 2410 2463 669649392 669649445 5.310000e-09 73.1
37 TraesCS3D01G189900 chr2B 94.444 36 2 0 1231 1266 92995616 92995651 5.350000e-04 56.5
38 TraesCS3D01G189900 chr7B 79.412 136 23 4 2123 2254 643462619 643462753 1.470000e-14 91.6


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 TraesCS3D01G189900 chr3D 177776865 177780699 3834 False 7083.00 7083 100.000000 1 3835 1 chr3D.!!$F1 3834
1 TraesCS3D01G189900 chr3B 256432083 256435566 3483 False 1462.00 3354 89.987667 1 3122 3 chr3B.!!$F2 3121
2 TraesCS3D01G189900 chr3B 256450336 256450947 611 False 795.00 795 90.554000 3120 3716 1 chr3B.!!$F1 596
3 TraesCS3D01G189900 chr3A 218726218 218731099 4881 False 1316.75 3053 92.471250 1 3835 4 chr3A.!!$F2 3834

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
440 1497 0.033504 AATGTGCCTACGCCTATCGG 59.966 55.0 0.0 0.0 43.86 4.18 F
565 1696 0.110486 GTGGCTTCCCAAGACCAAGA 59.890 55.0 0.0 0.0 44.33 3.02 F
708 1839 0.250338 GGACGACCTCCTTGTTTGCT 60.250 55.0 0.0 0.0 35.89 3.91 F
2065 3622 0.238553 GTGGCTCACGGCTTTTCTTC 59.761 55.0 0.0 0.0 41.46 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1690 3218 0.250901 TCAAACTGGCTTGGGCTCTC 60.251 55.0 0.00 0.0 38.73 3.20 R
1691 3219 0.538287 GTCAAACTGGCTTGGGCTCT 60.538 55.0 0.00 0.0 38.73 4.09 R
2159 3717 0.747644 TAGCGTCGATCACCGGGTAA 60.748 55.0 6.32 0.0 39.14 2.85 R
3808 5396 0.684535 TTTGGCTCTCCATGTGTCGA 59.315 50.0 0.00 0.0 43.05 4.20 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
97 98 4.158025 ACATGCCTGTCTAGTGTACTGTAC 59.842 45.833 10.98 10.98 0.00 2.90
102 103 5.647225 GCCTGTCTAGTGTACTGTACTACTT 59.353 44.000 17.98 4.85 0.00 2.24
143 144 1.755008 CTCCCGTGGGTCTCTCCTC 60.755 68.421 4.53 0.00 36.47 3.71
144 145 2.760385 CCCGTGGGTCTCTCCTCC 60.760 72.222 0.00 0.00 36.25 4.30
145 146 3.141488 CCGTGGGTCTCTCCTCCG 61.141 72.222 0.00 0.00 36.25 4.63
146 147 2.361357 CGTGGGTCTCTCCTCCGT 60.361 66.667 0.00 0.00 36.25 4.69
147 148 2.408241 CGTGGGTCTCTCCTCCGTC 61.408 68.421 0.00 0.00 36.25 4.79
148 149 2.053277 GTGGGTCTCTCCTCCGTCC 61.053 68.421 0.00 0.00 36.25 4.79
149 150 2.239439 TGGGTCTCTCCTCCGTCCT 61.239 63.158 0.00 0.00 36.25 3.85
178 1198 1.374125 CCGGAAGTGATCACGCACA 60.374 57.895 19.85 0.00 41.19 4.57
179 1199 1.626654 CCGGAAGTGATCACGCACAC 61.627 60.000 19.85 10.37 41.19 3.82
181 1201 1.071605 GGAAGTGATCACGCACACTC 58.928 55.000 19.85 10.42 44.94 3.51
311 1356 1.202758 TGTCCTCCCATGTCACAACAC 60.203 52.381 0.00 0.00 38.48 3.32
320 1365 0.035534 TGTCACAACACTGCACCTGT 60.036 50.000 0.00 0.00 0.00 4.00
347 1392 3.935203 ACTCGTGCCATTAGATTCAGTTG 59.065 43.478 0.00 0.00 0.00 3.16
349 1394 2.223340 CGTGCCATTAGATTCAGTTGCC 60.223 50.000 0.00 0.00 0.00 4.52
350 1395 2.754552 GTGCCATTAGATTCAGTTGCCA 59.245 45.455 0.00 0.00 0.00 4.92
351 1396 3.193267 GTGCCATTAGATTCAGTTGCCAA 59.807 43.478 0.00 0.00 0.00 4.52
352 1397 4.025360 TGCCATTAGATTCAGTTGCCAAT 58.975 39.130 0.00 0.00 0.00 3.16
353 1398 4.142116 TGCCATTAGATTCAGTTGCCAATG 60.142 41.667 0.00 0.00 0.00 2.82
354 1399 4.738541 GCCATTAGATTCAGTTGCCAATGG 60.739 45.833 0.00 0.00 42.39 3.16
392 1449 4.561105 GACCGTTCATGAGAAGAAGAACT 58.439 43.478 0.00 0.00 38.50 3.01
422 1479 5.182950 TCTTGAGTTTGTCTTTGTTCTGCAA 59.817 36.000 0.00 0.00 34.87 4.08
431 1488 3.253188 TCTTTGTTCTGCAATGTGCCTAC 59.747 43.478 0.00 0.00 44.23 3.18
437 1494 0.180171 TGCAATGTGCCTACGCCTAT 59.820 50.000 0.00 0.00 44.23 2.57
438 1495 0.868406 GCAATGTGCCTACGCCTATC 59.132 55.000 0.00 0.00 37.42 2.08
439 1496 1.139989 CAATGTGCCTACGCCTATCG 58.860 55.000 0.00 0.00 45.38 2.92
440 1497 0.033504 AATGTGCCTACGCCTATCGG 59.966 55.000 0.00 0.00 43.86 4.18
447 1504 2.940527 GCCTACGCCTATCGGTCTATCT 60.941 54.545 0.00 0.00 43.86 1.98
524 1590 2.680913 GCGCACACAGGTGGACATC 61.681 63.158 0.30 0.00 45.38 3.06
525 1591 1.301637 CGCACACAGGTGGACATCA 60.302 57.895 4.24 0.00 45.38 3.07
526 1592 1.293963 CGCACACAGGTGGACATCAG 61.294 60.000 4.24 0.00 45.38 2.90
561 1692 1.603739 GTGGTGGCTTCCCAAGACC 60.604 63.158 0.00 0.00 44.33 3.85
562 1693 2.081787 TGGTGGCTTCCCAAGACCA 61.082 57.895 0.00 0.00 44.33 4.02
563 1694 1.152830 GGTGGCTTCCCAAGACCAA 59.847 57.895 0.00 0.00 44.33 3.67
564 1695 0.895559 GGTGGCTTCCCAAGACCAAG 60.896 60.000 0.00 0.00 44.33 3.61
565 1696 0.110486 GTGGCTTCCCAAGACCAAGA 59.890 55.000 0.00 0.00 44.33 3.02
566 1697 0.110486 TGGCTTCCCAAGACCAAGAC 59.890 55.000 0.00 0.00 38.46 3.01
626 1757 3.003480 CCAAATCCAAACCGAGAGAGAC 58.997 50.000 0.00 0.00 0.00 3.36
627 1758 3.003480 CAAATCCAAACCGAGAGAGACC 58.997 50.000 0.00 0.00 0.00 3.85
689 1820 4.838486 GACGAGCCAGCGAGACGG 62.838 72.222 0.00 0.00 34.83 4.79
692 1823 4.500116 GAGCCAGCGAGACGGGAC 62.500 72.222 0.00 0.00 35.22 4.46
706 1837 2.928416 GGGACGACCTCCTTGTTTG 58.072 57.895 3.44 0.00 39.39 2.93
707 1838 1.235281 GGGACGACCTCCTTGTTTGC 61.235 60.000 3.44 0.00 39.39 3.68
708 1839 0.250338 GGACGACCTCCTTGTTTGCT 60.250 55.000 0.00 0.00 35.89 3.91
758 1899 4.752879 TCTACAACCGCTGGCCGC 62.753 66.667 9.20 9.20 35.03 6.53
789 1930 1.595109 CAGAACACAGCCACTCGCA 60.595 57.895 0.00 0.00 41.38 5.10
898 2044 0.980231 AGCATTCCTTCCCTCTCGCT 60.980 55.000 0.00 0.00 0.00 4.93
902 2048 1.032657 TTCCTTCCCTCTCGCTCTCG 61.033 60.000 0.00 0.00 0.00 4.04
915 2061 1.805428 GCTCTCGCTCCTCCATCTCC 61.805 65.000 0.00 0.00 0.00 3.71
916 2062 1.514678 CTCTCGCTCCTCCATCTCCG 61.515 65.000 0.00 0.00 0.00 4.63
918 2064 1.379977 TCGCTCCTCCATCTCCGTT 60.380 57.895 0.00 0.00 0.00 4.44
920 2066 0.528684 CGCTCCTCCATCTCCGTTTC 60.529 60.000 0.00 0.00 0.00 2.78
921 2067 0.528684 GCTCCTCCATCTCCGTTTCG 60.529 60.000 0.00 0.00 0.00 3.46
1091 2587 1.065709 GGTCCTCGCCCATTTACTCAA 60.066 52.381 0.00 0.00 0.00 3.02
1281 2781 2.608261 CGTCAAGGTCAGTCAGTTCCTC 60.608 54.545 0.00 0.00 0.00 3.71
1291 2803 2.635427 AGTCAGTTCCTCAGTTCCTTCC 59.365 50.000 0.00 0.00 0.00 3.46
1292 2804 1.978580 TCAGTTCCTCAGTTCCTTCCC 59.021 52.381 0.00 0.00 0.00 3.97
1488 3001 4.052159 AGCTACTCCATTCATGTTCGAG 57.948 45.455 0.00 0.00 0.00 4.04
1505 3018 2.270527 GCCAAGAGTCCTGGCTCC 59.729 66.667 23.22 0.00 44.72 4.70
1531 3044 5.277345 CGCTCTAATTAAACTGGCATACCAC 60.277 44.000 0.00 0.00 42.67 4.16
1534 3047 6.477253 TCTAATTAAACTGGCATACCACACA 58.523 36.000 0.00 0.00 42.67 3.72
1627 3146 1.947456 GGGGGCTTTTACGAGCAATAG 59.053 52.381 0.00 0.00 44.49 1.73
1635 3154 6.532657 GGCTTTTACGAGCAATAGTACTGTTA 59.467 38.462 5.39 0.00 44.49 2.41
1655 3183 7.773690 ACTGTTATTAACTCTCTCTCTCTCTCC 59.226 40.741 7.99 0.00 0.00 3.71
1680 3208 1.294780 CTCCCTGCTGTGGTGAGAC 59.705 63.158 0.00 0.00 30.84 3.36
1683 3211 1.750930 CCTGCTGTGGTGAGACTGT 59.249 57.895 0.00 0.00 0.00 3.55
1685 3213 0.390492 CTGCTGTGGTGAGACTGTGA 59.610 55.000 0.00 0.00 0.00 3.58
1687 3215 0.676184 GCTGTGGTGAGACTGTGAGA 59.324 55.000 0.00 0.00 0.00 3.27
1688 3216 1.336702 GCTGTGGTGAGACTGTGAGAG 60.337 57.143 0.00 0.00 0.00 3.20
1689 3217 1.959985 CTGTGGTGAGACTGTGAGAGT 59.040 52.381 0.00 0.00 37.76 3.24
1690 3218 1.683385 TGTGGTGAGACTGTGAGAGTG 59.317 52.381 0.00 0.00 33.83 3.51
1691 3219 1.957177 GTGGTGAGACTGTGAGAGTGA 59.043 52.381 0.00 0.00 33.83 3.41
1692 3220 2.030363 GTGGTGAGACTGTGAGAGTGAG 60.030 54.545 0.00 0.00 33.83 3.51
1693 3221 2.158608 TGGTGAGACTGTGAGAGTGAGA 60.159 50.000 0.00 0.00 33.83 3.27
1694 3222 2.487762 GGTGAGACTGTGAGAGTGAGAG 59.512 54.545 0.00 0.00 33.83 3.20
1695 3223 2.095263 GTGAGACTGTGAGAGTGAGAGC 60.095 54.545 0.00 0.00 33.83 4.09
1696 3224 1.472480 GAGACTGTGAGAGTGAGAGCC 59.528 57.143 0.00 0.00 33.83 4.70
1737 3270 5.345702 TGATATGTACACGAGCACCTTTAC 58.654 41.667 0.00 0.00 0.00 2.01
1790 3332 2.048503 GTAGCGACACGGCCAAGT 60.049 61.111 2.24 0.00 0.00 3.16
1931 3477 3.408020 GTGGCGCGCGACAACTAA 61.408 61.111 43.30 16.02 33.39 2.24
2017 3563 2.625823 CCCGCGCACAACCAATTCT 61.626 57.895 8.75 0.00 0.00 2.40
2040 3597 2.246719 TTTCAAACCCCAAAATGCGG 57.753 45.000 0.00 0.00 0.00 5.69
2065 3622 0.238553 GTGGCTCACGGCTTTTCTTC 59.761 55.000 0.00 0.00 41.46 2.87
2177 3735 2.048023 TTACCCGGTGATCGACGCT 61.048 57.895 0.00 0.00 42.43 5.07
2276 3834 1.903183 GTCTCCTACCAGTTCAAGGCT 59.097 52.381 0.00 0.00 0.00 4.58
2486 4044 3.246112 ACGCCCAGGCTGTACCAA 61.246 61.111 14.43 0.00 43.14 3.67
2564 4122 4.329545 GCCTGCCCGAACACTCCA 62.330 66.667 0.00 0.00 0.00 3.86
2570 4128 1.738099 CCCGAACACTCCAGCTTCG 60.738 63.158 0.00 0.00 37.20 3.79
2620 4178 1.928653 CGTTCAAGTTCGACGGCAA 59.071 52.632 0.00 0.00 33.45 4.52
2735 4293 3.517901 TGACCAACCCGATCAAGTTCTAT 59.482 43.478 0.00 0.00 0.00 1.98
2849 4407 0.108138 CGTGAGGGTTCATCCAGGAC 60.108 60.000 0.00 0.00 38.11 3.85
2855 4413 1.450312 GTTCATCCAGGACCGCCAG 60.450 63.158 0.00 0.00 36.29 4.85
2856 4414 3.329542 TTCATCCAGGACCGCCAGC 62.330 63.158 0.00 0.00 36.29 4.85
3230 4800 0.460284 AAGCGTTACATCTGGCCTCG 60.460 55.000 3.32 0.00 0.00 4.63
3262 4832 8.880878 AAATAACATAACCAAACCAAGTCAAC 57.119 30.769 0.00 0.00 0.00 3.18
3266 4836 6.279882 ACATAACCAAACCAAGTCAACAATG 58.720 36.000 0.00 0.00 0.00 2.82
3428 5000 5.456822 GCACAAAGTTTGAGTTGATGAGAAC 59.543 40.000 22.23 0.00 0.00 3.01
3442 5014 8.826765 AGTTGATGAGAACTCCCTCTTAAAATA 58.173 33.333 0.00 0.00 29.85 1.40
3541 5113 4.941873 CGAAGGAGGCCTTACTTGTTAATT 59.058 41.667 23.55 2.92 44.82 1.40
3595 5167 4.263462 ACCAATGCACTTAGTCAATCTCCA 60.263 41.667 0.00 0.00 0.00 3.86
3623 5211 2.809010 GCTCCTCCTAGTGTCGCC 59.191 66.667 0.00 0.00 0.00 5.54
3691 5279 4.776322 CCCGGCTCCATTGCACGA 62.776 66.667 0.00 0.00 34.04 4.35
3721 5309 1.750018 CGTGCTGGCATGGATCCAA 60.750 57.895 20.67 0.17 32.41 3.53
3723 5311 0.682209 GTGCTGGCATGGATCCAACT 60.682 55.000 20.67 0.00 32.41 3.16
3724 5312 0.681887 TGCTGGCATGGATCCAACTG 60.682 55.000 20.67 14.90 32.41 3.16
3725 5313 0.394762 GCTGGCATGGATCCAACTGA 60.395 55.000 20.67 2.54 32.41 3.41
3726 5314 1.753141 GCTGGCATGGATCCAACTGAT 60.753 52.381 20.67 0.00 36.01 2.90
3727 5315 2.487805 GCTGGCATGGATCCAACTGATA 60.488 50.000 20.67 5.29 32.41 2.15
3728 5316 3.824133 CTGGCATGGATCCAACTGATAA 58.176 45.455 20.67 2.08 32.41 1.75
3729 5317 3.554934 TGGCATGGATCCAACTGATAAC 58.445 45.455 20.67 5.80 32.41 1.89
3730 5318 2.887152 GGCATGGATCCAACTGATAACC 59.113 50.000 20.67 6.27 32.41 2.85
3731 5319 3.435601 GGCATGGATCCAACTGATAACCT 60.436 47.826 20.67 0.00 32.41 3.50
3732 5320 4.202461 GGCATGGATCCAACTGATAACCTA 60.202 45.833 20.67 0.00 32.41 3.08
3733 5321 4.757149 GCATGGATCCAACTGATAACCTAC 59.243 45.833 20.67 0.00 32.41 3.18
3734 5322 5.687441 GCATGGATCCAACTGATAACCTACA 60.687 44.000 20.67 0.00 32.41 2.74
3735 5323 6.356556 CATGGATCCAACTGATAACCTACAA 58.643 40.000 20.67 0.00 32.41 2.41
3736 5324 5.989477 TGGATCCAACTGATAACCTACAAG 58.011 41.667 13.46 0.00 32.41 3.16
3737 5325 5.487488 TGGATCCAACTGATAACCTACAAGT 59.513 40.000 13.46 0.00 32.41 3.16
3738 5326 6.670464 TGGATCCAACTGATAACCTACAAGTA 59.330 38.462 13.46 0.00 32.41 2.24
3775 5363 6.790319 AGTATAGGGGATCACAACAGTTTTT 58.210 36.000 0.00 0.00 0.00 1.94
3783 5371 5.300792 GGATCACAACAGTTTTTGAGGGTAA 59.699 40.000 0.00 0.00 0.00 2.85
3816 5404 7.169158 ACCCAAATTTATTGATTCGACACAT 57.831 32.000 0.00 0.00 0.00 3.21
3817 5405 7.035004 ACCCAAATTTATTGATTCGACACATG 58.965 34.615 0.00 0.00 0.00 3.21
3819 5407 7.257003 CCAAATTTATTGATTCGACACATGGA 58.743 34.615 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
97 98 1.747355 CAAGGCATGGGAGCAAAGTAG 59.253 52.381 0.00 0.00 35.83 2.57
102 103 2.117858 TGCAAGGCATGGGAGCAA 59.882 55.556 0.00 0.00 31.71 3.91
143 144 2.024871 GCGTGATCGAGAGGACGG 59.975 66.667 9.44 0.00 39.71 4.79
144 145 2.024871 GGCGTGATCGAGAGGACG 59.975 66.667 0.00 0.00 39.71 4.79
145 146 2.024871 CGGCGTGATCGAGAGGAC 59.975 66.667 0.00 0.00 39.71 3.85
146 147 3.209812 CCGGCGTGATCGAGAGGA 61.210 66.667 6.01 0.00 39.71 3.71
147 148 2.669808 CTTCCGGCGTGATCGAGAGG 62.670 65.000 6.01 0.00 39.71 3.69
148 149 1.298713 CTTCCGGCGTGATCGAGAG 60.299 63.158 6.01 0.00 39.71 3.20
149 150 2.044555 ACTTCCGGCGTGATCGAGA 61.045 57.895 6.01 0.00 39.71 4.04
311 1356 0.603569 ACGAGTAGGAACAGGTGCAG 59.396 55.000 0.00 0.00 0.00 4.41
320 1365 4.404394 TGAATCTAATGGCACGAGTAGGAA 59.596 41.667 0.00 0.00 0.00 3.36
349 1394 3.190327 TCGGTTGATTGTTAGTGCCATTG 59.810 43.478 0.00 0.00 0.00 2.82
350 1395 3.190535 GTCGGTTGATTGTTAGTGCCATT 59.809 43.478 0.00 0.00 0.00 3.16
351 1396 2.747446 GTCGGTTGATTGTTAGTGCCAT 59.253 45.455 0.00 0.00 0.00 4.40
352 1397 2.147958 GTCGGTTGATTGTTAGTGCCA 58.852 47.619 0.00 0.00 0.00 4.92
353 1398 1.467342 GGTCGGTTGATTGTTAGTGCC 59.533 52.381 0.00 0.00 0.00 5.01
354 1399 1.127951 CGGTCGGTTGATTGTTAGTGC 59.872 52.381 0.00 0.00 0.00 4.40
355 1400 2.409975 ACGGTCGGTTGATTGTTAGTG 58.590 47.619 0.00 0.00 0.00 2.74
356 1401 2.825861 ACGGTCGGTTGATTGTTAGT 57.174 45.000 0.00 0.00 0.00 2.24
357 1402 3.061322 TGAACGGTCGGTTGATTGTTAG 58.939 45.455 0.00 0.00 39.50 2.34
358 1403 3.109044 TGAACGGTCGGTTGATTGTTA 57.891 42.857 0.00 0.00 39.50 2.41
359 1404 1.956297 TGAACGGTCGGTTGATTGTT 58.044 45.000 0.00 0.00 39.50 2.83
360 1405 1.804151 CATGAACGGTCGGTTGATTGT 59.196 47.619 0.00 0.00 39.50 2.71
366 1423 1.616865 TCTTCTCATGAACGGTCGGTT 59.383 47.619 0.00 0.00 42.96 4.44
392 1449 5.253330 ACAAAGACAAACTCAAGACCTTGA 58.747 37.500 11.47 11.47 46.27 3.02
437 1494 4.197750 GTCACCTACAAGAGATAGACCGA 58.802 47.826 0.00 0.00 0.00 4.69
438 1495 3.002451 CGTCACCTACAAGAGATAGACCG 59.998 52.174 0.00 0.00 0.00 4.79
439 1496 4.197750 TCGTCACCTACAAGAGATAGACC 58.802 47.826 0.00 0.00 0.00 3.85
440 1497 5.814764 TTCGTCACCTACAAGAGATAGAC 57.185 43.478 0.00 0.00 0.00 2.59
447 1504 1.403647 CGCCATTCGTCACCTACAAGA 60.404 52.381 0.00 0.00 0.00 3.02
506 1572 2.669569 ATGTCCACCTGTGTGCGC 60.670 61.111 0.00 0.00 41.35 6.09
507 1573 1.293963 CTGATGTCCACCTGTGTGCG 61.294 60.000 0.00 0.00 41.35 5.34
508 1574 0.250467 ACTGATGTCCACCTGTGTGC 60.250 55.000 0.00 0.00 41.35 4.57
509 1575 1.202687 ACACTGATGTCCACCTGTGTG 60.203 52.381 3.77 0.00 41.62 3.82
510 1576 1.131638 ACACTGATGTCCACCTGTGT 58.868 50.000 0.00 0.00 39.51 3.72
521 1587 0.371301 CACGATTCGGCACACTGATG 59.629 55.000 11.29 0.00 0.00 3.07
524 1590 3.168271 CCACGATTCGGCACACTG 58.832 61.111 11.29 0.00 0.00 3.66
561 1692 1.128200 TGTCCATATCGGGGGTCTTG 58.872 55.000 0.00 0.00 34.36 3.02
562 1693 1.129058 GTGTCCATATCGGGGGTCTT 58.871 55.000 0.00 0.00 34.36 3.01
563 1694 0.031515 TGTGTCCATATCGGGGGTCT 60.032 55.000 0.00 0.00 34.36 3.85
564 1695 1.002087 GATGTGTCCATATCGGGGGTC 59.998 57.143 0.00 0.00 34.36 4.46
565 1696 1.056660 GATGTGTCCATATCGGGGGT 58.943 55.000 0.00 0.00 34.36 4.95
566 1697 1.055849 TGATGTGTCCATATCGGGGG 58.944 55.000 0.52 0.00 32.42 5.40
626 1757 1.005347 GCACGATTCGTTTATGGTCGG 60.005 52.381 9.40 0.00 38.32 4.79
627 1758 1.005347 GGCACGATTCGTTTATGGTCG 60.005 52.381 9.40 0.00 38.32 4.79
690 1821 1.264288 CAAGCAAACAAGGAGGTCGTC 59.736 52.381 0.00 0.00 0.00 4.20
691 1822 1.308998 CAAGCAAACAAGGAGGTCGT 58.691 50.000 0.00 0.00 0.00 4.34
692 1823 0.040067 GCAAGCAAACAAGGAGGTCG 60.040 55.000 0.00 0.00 0.00 4.79
693 1824 1.322442 AGCAAGCAAACAAGGAGGTC 58.678 50.000 0.00 0.00 0.00 3.85
705 1836 1.376466 GAGGAGGGACAAGCAAGCA 59.624 57.895 0.00 0.00 0.00 3.91
706 1837 1.377856 GGAGGAGGGACAAGCAAGC 60.378 63.158 0.00 0.00 0.00 4.01
707 1838 1.301293 GGGAGGAGGGACAAGCAAG 59.699 63.158 0.00 0.00 0.00 4.01
708 1839 2.231380 GGGGAGGAGGGACAAGCAA 61.231 63.158 0.00 0.00 0.00 3.91
758 1899 2.974148 TTCTGTGCTGCACCTGCG 60.974 61.111 28.17 14.60 45.83 5.18
898 2044 1.527148 CGGAGATGGAGGAGCGAGA 60.527 63.158 0.00 0.00 0.00 4.04
902 2048 0.528684 CGAAACGGAGATGGAGGAGC 60.529 60.000 0.00 0.00 0.00 4.70
915 2061 0.385598 TGAGACTGCGAGACGAAACG 60.386 55.000 0.00 0.00 0.00 3.60
916 2062 1.716581 CTTGAGACTGCGAGACGAAAC 59.283 52.381 0.00 0.00 0.00 2.78
918 2064 1.235724 TCTTGAGACTGCGAGACGAA 58.764 50.000 0.00 0.00 0.00 3.85
920 2066 1.131315 TGATCTTGAGACTGCGAGACG 59.869 52.381 0.00 0.00 31.35 4.18
921 2067 2.796304 CTGATCTTGAGACTGCGAGAC 58.204 52.381 0.00 0.00 31.35 3.36
1281 2781 1.405661 GCGAGGTTAGGGAAGGAACTG 60.406 57.143 0.00 0.00 40.86 3.16
1291 2803 4.176752 GGGCAGGGCGAGGTTAGG 62.177 72.222 0.00 0.00 0.00 2.69
1292 2804 4.176752 GGGGCAGGGCGAGGTTAG 62.177 72.222 0.00 0.00 0.00 2.34
1505 3018 5.177696 GGTATGCCAGTTTAATTAGAGCGAG 59.822 44.000 0.00 0.00 34.09 5.03
1531 3044 3.557595 GGAGAAAGGCGATCTGTATTGTG 59.442 47.826 0.00 0.00 0.00 3.33
1534 3047 3.041946 AGGGAGAAAGGCGATCTGTATT 58.958 45.455 0.00 0.00 0.00 1.89
1627 3146 9.609346 AGAGAGAGAGAGAGTTAATAACAGTAC 57.391 37.037 5.89 0.00 0.00 2.73
1635 3154 5.672194 AGAGGGAGAGAGAGAGAGAGTTAAT 59.328 44.000 0.00 0.00 0.00 1.40
1638 3157 3.456277 GAGAGGGAGAGAGAGAGAGAGTT 59.544 52.174 0.00 0.00 0.00 3.01
1640 3159 3.041211 TGAGAGGGAGAGAGAGAGAGAG 58.959 54.545 0.00 0.00 0.00 3.20
1641 3160 2.771943 GTGAGAGGGAGAGAGAGAGAGA 59.228 54.545 0.00 0.00 0.00 3.10
1655 3183 1.595882 CACAGCAGGGAGTGAGAGG 59.404 63.158 0.00 0.00 37.97 3.69
1680 3208 0.972134 TTGGGCTCTCACTCTCACAG 59.028 55.000 0.00 0.00 0.00 3.66
1683 3211 1.548357 GGCTTGGGCTCTCACTCTCA 61.548 60.000 0.00 0.00 38.73 3.27
1685 3213 1.537397 TGGCTTGGGCTCTCACTCT 60.537 57.895 0.00 0.00 38.73 3.24
1687 3215 1.422161 AACTGGCTTGGGCTCTCACT 61.422 55.000 0.00 0.00 38.73 3.41
1688 3216 0.538287 AAACTGGCTTGGGCTCTCAC 60.538 55.000 0.00 0.00 38.73 3.51
1689 3217 0.538057 CAAACTGGCTTGGGCTCTCA 60.538 55.000 0.00 0.00 38.73 3.27
1690 3218 0.250901 TCAAACTGGCTTGGGCTCTC 60.251 55.000 0.00 0.00 38.73 3.20
1691 3219 0.538287 GTCAAACTGGCTTGGGCTCT 60.538 55.000 0.00 0.00 38.73 4.09
1692 3220 0.538287 AGTCAAACTGGCTTGGGCTC 60.538 55.000 0.00 0.00 38.73 4.70
1693 3221 0.825010 CAGTCAAACTGGCTTGGGCT 60.825 55.000 0.00 0.00 42.35 5.19
1694 3222 1.662044 CAGTCAAACTGGCTTGGGC 59.338 57.895 0.00 0.00 42.35 5.36
1790 3332 8.308931 TCTAGTATTTCTCGCCTTGTTTTCTTA 58.691 33.333 0.00 0.00 0.00 2.10
1927 3473 2.966309 GCGCGGCAGCTTTGTTAGT 61.966 57.895 8.83 0.00 42.32 2.24
2006 3552 6.995686 GGGGTTTGAAATTTAGAATTGGTTGT 59.004 34.615 0.00 0.00 0.00 3.32
2010 3556 8.457238 TTTTGGGGTTTGAAATTTAGAATTGG 57.543 30.769 0.00 0.00 0.00 3.16
2011 3557 9.896263 CATTTTGGGGTTTGAAATTTAGAATTG 57.104 29.630 0.00 0.00 0.00 2.32
2012 3558 8.575589 GCATTTTGGGGTTTGAAATTTAGAATT 58.424 29.630 0.00 0.00 0.00 2.17
2017 3563 4.757149 CCGCATTTTGGGGTTTGAAATTTA 59.243 37.500 2.63 0.00 44.53 1.40
2055 3612 2.164219 TCATCGCATTGGAAGAAAAGCC 59.836 45.455 0.00 0.00 0.00 4.35
2065 3622 2.094906 CCCTGCATTATCATCGCATTGG 60.095 50.000 0.00 0.00 34.63 3.16
2159 3717 0.747644 TAGCGTCGATCACCGGGTAA 60.748 55.000 6.32 0.00 39.14 2.85
2177 3735 1.066422 CTCGAGCTGCGCCTTGATA 59.934 57.895 4.18 0.00 40.61 2.15
2276 3834 2.922503 TCCACCTGCCAGAGCGAA 60.923 61.111 0.00 0.00 44.31 4.70
2564 4122 3.292936 ACCGTGGACGTCGAAGCT 61.293 61.111 9.92 0.00 37.74 3.74
2620 4178 2.605257 TCTGCAGGTTGGTGTAGTAGT 58.395 47.619 15.13 0.00 32.42 2.73
2735 4293 2.268920 GACATGGAGAAGGCGGCA 59.731 61.111 13.08 0.00 0.00 5.69
2849 4407 1.137404 CCAAGAAAATCGCTGGCGG 59.863 57.895 14.94 0.00 40.25 6.13
2964 4531 1.736126 CATACTCAGGCACAGCACTTG 59.264 52.381 0.00 0.00 0.00 3.16
3223 4790 7.280652 GGTTATGTTATTTTAGTTACGAGGCCA 59.719 37.037 5.01 0.00 0.00 5.36
3307 4879 4.649674 AGATGTCGCTCCTACATTTTAGGA 59.350 41.667 0.00 0.00 41.14 2.94
3428 5000 7.176690 TCCTTTGCACTTTATTTTAAGAGGGAG 59.823 37.037 0.00 0.00 0.00 4.30
3709 5297 2.887152 GGTTATCAGTTGGATCCATGCC 59.113 50.000 17.06 6.87 37.44 4.40
3721 5309 8.648693 GGGTTATCATACTTGTAGGTTATCAGT 58.351 37.037 0.00 0.00 0.00 3.41
3723 5311 8.426489 GTGGGTTATCATACTTGTAGGTTATCA 58.574 37.037 0.00 0.00 0.00 2.15
3724 5312 8.426489 TGTGGGTTATCATACTTGTAGGTTATC 58.574 37.037 0.00 0.00 0.00 1.75
3725 5313 8.326765 TGTGGGTTATCATACTTGTAGGTTAT 57.673 34.615 0.00 0.00 0.00 1.89
3726 5314 7.736881 TGTGGGTTATCATACTTGTAGGTTA 57.263 36.000 0.00 0.00 0.00 2.85
3727 5315 6.630203 TGTGGGTTATCATACTTGTAGGTT 57.370 37.500 0.00 0.00 0.00 3.50
3728 5316 6.214819 ACTTGTGGGTTATCATACTTGTAGGT 59.785 38.462 0.00 0.00 0.00 3.08
3729 5317 6.650120 ACTTGTGGGTTATCATACTTGTAGG 58.350 40.000 0.00 0.00 0.00 3.18
3732 5320 8.429641 CCTATACTTGTGGGTTATCATACTTGT 58.570 37.037 0.00 0.00 0.00 3.16
3733 5321 7.878127 CCCTATACTTGTGGGTTATCATACTTG 59.122 40.741 0.00 0.00 36.32 3.16
3734 5322 7.017254 CCCCTATACTTGTGGGTTATCATACTT 59.983 40.741 0.00 0.00 39.31 2.24
3735 5323 6.500751 CCCCTATACTTGTGGGTTATCATACT 59.499 42.308 0.00 0.00 39.31 2.12
3736 5324 6.499350 TCCCCTATACTTGTGGGTTATCATAC 59.501 42.308 0.00 0.00 39.31 2.39
3737 5325 6.636003 TCCCCTATACTTGTGGGTTATCATA 58.364 40.000 0.00 0.00 39.31 2.15
3738 5326 5.482580 TCCCCTATACTTGTGGGTTATCAT 58.517 41.667 0.00 0.00 39.31 2.45
3764 5352 7.891498 ATACTTTACCCTCAAAAACTGTTGT 57.109 32.000 0.00 0.00 0.00 3.32
3808 5396 0.684535 TTTGGCTCTCCATGTGTCGA 59.315 50.000 0.00 0.00 43.05 4.20
3809 5397 1.742761 ATTTGGCTCTCCATGTGTCG 58.257 50.000 0.00 0.00 43.05 4.35


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

AutoCloner maintained by Alex Coulton.