Multiple sequence alignment - TraesCS5A01G280400

Loading Multiple Alignment...

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 TraesCS5A01G280400 chr5A 100.000 3780 0 0 1 3780 489788848 489792627 0.000000e+00 6981.0
1 TraesCS5A01G280400 chr5D 92.884 1321 69 11 1739 3049 386984052 386985357 0.000000e+00 1895.0
2 TraesCS5A01G280400 chr5D 89.024 1312 73 39 453 1736 386982693 386983961 0.000000e+00 1559.0
3 TraesCS5A01G280400 chr5D 83.146 267 38 7 1 265 386982033 386982294 1.760000e-58 237.0
4 TraesCS5A01G280400 chr5B 90.445 921 50 14 2128 3034 465231876 465232772 0.000000e+00 1179.0
5 TraesCS5A01G280400 chr5B 88.391 758 55 15 3045 3771 465232813 465233568 0.000000e+00 881.0
6 TraesCS5A01G280400 chr5B 94.007 534 27 3 647 1180 465230409 465230937 0.000000e+00 804.0
7 TraesCS5A01G280400 chr5B 89.831 531 29 11 1207 1716 465230936 465231462 0.000000e+00 658.0
8 TraesCS5A01G280400 chr5B 91.136 361 24 5 1748 2101 465231525 465231884 2.040000e-132 483.0
9 TraesCS5A01G280400 chr3D 79.233 313 49 14 2446 2755 38278400 38278699 1.780000e-48 204.0
10 TraesCS5A01G280400 chr3D 91.837 49 3 1 70 117 450240150 450240198 2.440000e-07 67.6
11 TraesCS5A01G280400 chr3D 96.875 32 1 0 3453 3484 577052612 577052581 2.000000e-03 54.7
12 TraesCS5A01G280400 chr7D 79.365 252 41 11 3273 3519 67094728 67094973 2.340000e-37 167.0
13 TraesCS5A01G280400 chr7A 77.947 263 45 13 3294 3551 72821676 72821422 6.540000e-33 152.0
14 TraesCS5A01G280400 chr7A 77.947 263 45 13 3294 3551 72859266 72859012 6.540000e-33 152.0
15 TraesCS5A01G280400 chr1D 77.372 274 51 9 189 456 55884117 55884385 6.540000e-33 152.0
16 TraesCS5A01G280400 chr2D 78.182 165 25 9 3324 3484 304136679 304136836 1.120000e-15 95.3
17 TraesCS5A01G280400 chr2B 100.000 32 0 0 635 666 37739756 37739787 4.080000e-05 60.2
18 TraesCS5A01G280400 chr6A 100.000 29 0 0 635 663 609880013 609879985 2.000000e-03 54.7


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 TraesCS5A01G280400 chr5A 489788848 489792627 3779 False 6981.000000 6981 100.000000 1 3780 1 chr5A.!!$F1 3779
1 TraesCS5A01G280400 chr5D 386982033 386985357 3324 False 1230.333333 1895 88.351333 1 3049 3 chr5D.!!$F1 3048
2 TraesCS5A01G280400 chr5B 465230409 465233568 3159 False 801.000000 1179 90.762000 647 3771 5 chr5B.!!$F1 3124

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
828 1060 0.820891 ATGATGCCCAGAACGATGCC 60.821 55.0 0.0 0.0 0.0 4.40 F
1658 1914 0.687354 TGTTCTGTCCCTTCCAGCTC 59.313 55.0 0.0 0.0 0.0 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1664 1920 0.689080 ACTGCATCTCGACCCCATCT 60.689 55.0 0.00 0.0 0.00 2.90 R
2927 3289 0.179073 AATCCGGAACAGATCGGCAG 60.179 55.0 9.01 0.0 45.31 4.85 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
24 25 3.422085 CCAAATTCGTGAGCATTTTTGCG 60.422 43.478 0.00 0.00 34.77 4.85
25 26 2.987413 ATTCGTGAGCATTTTTGCGA 57.013 40.000 0.00 0.00 40.27 5.10
30 31 3.668191 TCGTGAGCATTTTTGCGAAAATC 59.332 39.130 19.77 14.66 42.14 2.17
39 40 4.599047 TTTTGCGAAAATCTGGGAACAT 57.401 36.364 0.00 0.00 41.51 2.71
43 44 4.954875 TGCGAAAATCTGGGAACATTTTT 58.045 34.783 0.00 0.00 41.51 1.94
68 69 7.841915 TTTTCAAATCAGTGAACTTTTTCCC 57.158 32.000 0.00 0.00 37.24 3.97
70 71 6.537453 TCAAATCAGTGAACTTTTTCCCAA 57.463 33.333 0.00 0.00 0.00 4.12
71 72 7.123355 TCAAATCAGTGAACTTTTTCCCAAT 57.877 32.000 0.00 0.00 0.00 3.16
72 73 7.563906 TCAAATCAGTGAACTTTTTCCCAATT 58.436 30.769 0.00 0.00 0.00 2.32
74 75 5.275067 TCAGTGAACTTTTTCCCAATTGG 57.725 39.130 18.21 18.21 0.00 3.16
75 76 4.959210 TCAGTGAACTTTTTCCCAATTGGA 59.041 37.500 26.60 9.22 43.18 3.53
76 77 5.068987 TCAGTGAACTTTTTCCCAATTGGAG 59.931 40.000 26.60 16.48 46.24 3.86
84 85 8.028652 ACTTTTTCCCAATTGGAGACATTTTA 57.971 30.769 26.60 2.76 46.24 1.52
143 144 9.033481 TGTGTTCATCAGATTTTTCAAATGTTC 57.967 29.630 0.00 0.00 0.00 3.18
187 188 7.565450 TTAAACACGCTCAAAATGATCATTG 57.435 32.000 21.39 11.86 0.00 2.82
341 499 9.883142 AAGGTCATTGAGTTTAAATTTTGTTCA 57.117 25.926 0.00 0.00 0.00 3.18
407 583 8.998377 TCAATGAACGTTTTTCTGAGATTCATA 58.002 29.630 0.46 0.00 34.96 2.15
412 588 9.612620 GAACGTTTTTCTGAGATTCATAAATGT 57.387 29.630 0.46 0.00 30.09 2.71
473 684 6.510799 CGTGAACATCTTATGATTTCTGGAGC 60.511 42.308 0.00 0.00 0.00 4.70
660 890 1.154205 CCTCACGCGCCAAATAGGAG 61.154 60.000 5.73 0.36 41.22 3.69
666 896 1.227973 CGCCAAATAGGAGCTCCCC 60.228 63.158 29.54 6.19 41.22 4.81
667 897 1.151679 GCCAAATAGGAGCTCCCCC 59.848 63.158 29.54 5.32 41.22 5.40
668 898 1.451936 CCAAATAGGAGCTCCCCCG 59.548 63.158 29.54 13.13 41.22 5.73
669 899 1.345715 CCAAATAGGAGCTCCCCCGT 61.346 60.000 29.54 13.43 41.22 5.28
828 1060 0.820891 ATGATGCCCAGAACGATGCC 60.821 55.000 0.00 0.00 0.00 4.40
860 1092 1.428912 TCTTGTTCTTGGGGGCTCAAT 59.571 47.619 0.00 0.00 0.00 2.57
970 1202 2.301870 TCCTACCACATCACGAGCTTTT 59.698 45.455 0.00 0.00 0.00 2.27
1164 1396 2.821366 GTCCCGGCATGCAGTGAG 60.821 66.667 21.36 6.72 0.00 3.51
1168 1400 2.401766 CCGGCATGCAGTGAGGAAC 61.402 63.158 21.36 0.00 31.32 3.62
1223 1455 5.998454 ACTTCAAGTTCTGTCACAATCAG 57.002 39.130 0.00 0.00 0.00 2.90
1276 1508 2.555757 CAGGGCAAGGAAACTCTGAAAG 59.444 50.000 0.00 0.00 42.68 2.62
1277 1509 2.443255 AGGGCAAGGAAACTCTGAAAGA 59.557 45.455 0.00 0.00 43.69 2.52
1278 1510 3.117512 AGGGCAAGGAAACTCTGAAAGAA 60.118 43.478 0.00 0.00 46.34 2.52
1279 1511 3.636764 GGGCAAGGAAACTCTGAAAGAAA 59.363 43.478 0.00 0.00 46.34 2.52
1289 1525 6.496338 AACTCTGAAAGAAACTCGTGTTTT 57.504 33.333 15.98 1.59 46.34 2.43
1425 1661 1.219664 CATAACGGAGGCGAACCCA 59.780 57.895 0.00 0.00 36.11 4.51
1535 1771 5.485353 TCCCTCTCAACATCTTGATGTAACT 59.515 40.000 15.50 0.00 35.78 2.24
1539 1775 7.009631 CCTCTCAACATCTTGATGTAACTAACG 59.990 40.741 15.50 3.58 35.78 3.18
1540 1776 6.811665 TCTCAACATCTTGATGTAACTAACGG 59.188 38.462 15.50 3.17 35.78 4.44
1541 1777 6.693466 TCAACATCTTGATGTAACTAACGGA 58.307 36.000 15.50 3.20 33.81 4.69
1542 1778 6.811665 TCAACATCTTGATGTAACTAACGGAG 59.188 38.462 15.50 0.00 33.81 4.63
1543 1779 5.109903 ACATCTTGATGTAACTAACGGAGC 58.890 41.667 13.84 0.00 32.14 4.70
1544 1780 3.766151 TCTTGATGTAACTAACGGAGCG 58.234 45.455 0.00 0.00 0.00 5.03
1606 1862 2.376109 TGTAACCAAGCCGTCCAAAAA 58.624 42.857 0.00 0.00 0.00 1.94
1608 1864 1.480789 AACCAAGCCGTCCAAAAACT 58.519 45.000 0.00 0.00 0.00 2.66
1658 1914 0.687354 TGTTCTGTCCCTTCCAGCTC 59.313 55.000 0.00 0.00 0.00 4.09
1664 1920 1.078528 TCCCTTCCAGCTCTCCGAA 59.921 57.895 0.00 0.00 0.00 4.30
1670 1926 1.445095 CCAGCTCTCCGAAGATGGG 59.555 63.158 8.34 0.00 46.76 4.00
1700 1956 2.095059 GCAGTTCGCAACCAATCATCTT 60.095 45.455 0.00 0.00 41.79 2.40
1717 1973 9.860898 CAATCATCTTGGTATATATTGTCTCGA 57.139 33.333 0.00 0.00 0.00 4.04
1846 2190 1.153745 CACTGCTGAGTCTACGGGC 60.154 63.158 0.00 0.00 0.00 6.13
1867 2211 2.203070 GAGGGCCGCATCGTGAAT 60.203 61.111 1.02 0.00 0.00 2.57
2050 2400 2.256391 TGGACAATCCAAGCTTGCG 58.744 52.632 21.43 14.02 45.00 4.85
2095 2445 3.884091 TCTCTAGACGGCTCAAGGTATTC 59.116 47.826 0.00 0.00 0.00 1.75
2099 2449 4.287766 AGACGGCTCAAGGTATTCTTTT 57.712 40.909 0.00 0.00 32.41 2.27
2100 2450 4.254492 AGACGGCTCAAGGTATTCTTTTC 58.746 43.478 0.00 0.00 32.41 2.29
2101 2451 3.344515 ACGGCTCAAGGTATTCTTTTCC 58.655 45.455 0.00 0.00 32.41 3.13
2102 2452 3.009143 ACGGCTCAAGGTATTCTTTTCCT 59.991 43.478 0.00 0.00 32.41 3.36
2110 2460 6.445139 TCAAGGTATTCTTTTCCTCTCTCCAT 59.555 38.462 0.00 0.00 32.41 3.41
2120 2470 3.309296 TCCTCTCTCCATATTTTCGCCT 58.691 45.455 0.00 0.00 0.00 5.52
2121 2471 4.480115 TCCTCTCTCCATATTTTCGCCTA 58.520 43.478 0.00 0.00 0.00 3.93
2123 2473 5.544176 TCCTCTCTCCATATTTTCGCCTATT 59.456 40.000 0.00 0.00 0.00 1.73
2124 2474 6.724441 TCCTCTCTCCATATTTTCGCCTATTA 59.276 38.462 0.00 0.00 0.00 0.98
2125 2475 6.814146 CCTCTCTCCATATTTTCGCCTATTAC 59.186 42.308 0.00 0.00 0.00 1.89
2127 2477 6.497259 TCTCTCCATATTTTCGCCTATTACCT 59.503 38.462 0.00 0.00 0.00 3.08
2167 2518 6.322126 AGATCAATACTGAATAGAGGGCTCT 58.678 40.000 0.00 0.00 38.20 4.09
2177 2528 7.565398 ACTGAATAGAGGGCTCTTACTAATTGA 59.435 37.037 0.00 0.00 40.93 2.57
2213 2564 8.926715 AAAAGTTTCAAACTATTCTGAACCAC 57.073 30.769 2.38 0.00 41.91 4.16
2354 2705 2.037121 CCGGCCCATTTTTCTGTTCTTT 59.963 45.455 0.00 0.00 0.00 2.52
2394 2745 5.469373 TGTCATCAAGTTTTAGCTATGCG 57.531 39.130 0.00 0.00 0.00 4.73
2402 2753 5.828299 AGTTTTAGCTATGCGCCATTTTA 57.172 34.783 4.18 0.00 40.39 1.52
2435 2786 0.032952 TATGGCTCCACGGCGTTATC 59.967 55.000 11.19 0.00 42.02 1.75
2441 2792 2.538939 GCTCCACGGCGTTATCAATTTC 60.539 50.000 11.19 0.00 0.00 2.17
2444 2795 3.118702 TCCACGGCGTTATCAATTTCCTA 60.119 43.478 11.19 0.00 0.00 2.94
2509 2860 3.370633 GGAAGAATGTACCCCAGGTTCTC 60.371 52.174 0.00 0.00 37.09 2.87
2520 2871 2.763448 CCCAGGTTCTCCTCTACTCTTG 59.237 54.545 0.00 0.00 43.07 3.02
2526 2878 3.458044 TCTCCTCTACTCTTGCCTTCA 57.542 47.619 0.00 0.00 0.00 3.02
2617 2972 0.407139 ATTTCCAGGGAGCAGCAACT 59.593 50.000 0.00 0.00 0.00 3.16
2656 3011 1.316651 GCCATCAGCTGAAGGGAATC 58.683 55.000 32.92 16.69 38.99 2.52
2706 3061 1.740025 GGAGAAGACGAGCAAATTGGG 59.260 52.381 0.00 0.00 0.00 4.12
2799 3154 3.191539 GCAGGCGAGAGAAAGGCG 61.192 66.667 0.00 0.00 38.03 5.52
2884 3242 4.188247 TGTTTGGATCGTGACCTAAGAG 57.812 45.455 0.00 0.00 0.00 2.85
2885 3243 3.056107 TGTTTGGATCGTGACCTAAGAGG 60.056 47.826 0.00 0.00 42.49 3.69
2886 3244 1.112113 TGGATCGTGACCTAAGAGGC 58.888 55.000 0.00 0.00 39.63 4.70
2887 3245 1.342076 TGGATCGTGACCTAAGAGGCT 60.342 52.381 0.00 0.00 39.63 4.58
2888 3246 2.092049 TGGATCGTGACCTAAGAGGCTA 60.092 50.000 0.00 0.00 39.63 3.93
2889 3247 2.957006 GGATCGTGACCTAAGAGGCTAA 59.043 50.000 0.00 0.00 39.63 3.09
2890 3248 3.004944 GGATCGTGACCTAAGAGGCTAAG 59.995 52.174 0.00 0.00 39.63 2.18
2891 3249 3.361281 TCGTGACCTAAGAGGCTAAGA 57.639 47.619 0.00 0.00 39.63 2.10
2892 3250 3.015327 TCGTGACCTAAGAGGCTAAGAC 58.985 50.000 0.00 0.00 39.63 3.01
2927 3289 9.628500 ACCCTGGTTAAATTTCTCTAATGTATC 57.372 33.333 0.00 0.00 0.00 2.24
2936 3298 6.656632 TTTCTCTAATGTATCTGCCGATCT 57.343 37.500 0.00 0.00 0.00 2.75
2941 3303 2.890808 TGTATCTGCCGATCTGTTCC 57.109 50.000 0.00 0.00 0.00 3.62
2942 3304 1.067060 TGTATCTGCCGATCTGTTCCG 59.933 52.381 0.00 0.00 0.00 4.30
2951 3313 1.806623 CGATCTGTTCCGGATTGGGTC 60.807 57.143 4.15 3.02 38.76 4.46
3037 3409 6.061022 TCAGAGATATTTTGGTGTTGCCTA 57.939 37.500 0.00 0.00 38.35 3.93
3039 3411 7.118723 TCAGAGATATTTTGGTGTTGCCTAAT 58.881 34.615 0.00 0.00 38.35 1.73
3051 3453 5.235831 GGTGTTGCCTAATACTTTATCGTCC 59.764 44.000 0.00 0.00 0.00 4.79
3086 3488 3.391665 CTGATGGAGTCCCCGGTGC 62.392 68.421 6.74 0.00 37.93 5.01
3101 3503 4.015406 TGCGGGCACGTCCTGATT 62.015 61.111 11.45 0.00 44.37 2.57
3104 3506 1.227263 CGGGCACGTCCTGATTAGG 60.227 63.158 0.00 0.00 44.37 2.69
3146 3548 2.195139 GCAGGCAGCCAGATGGAT 59.805 61.111 15.80 0.00 37.39 3.41
3171 3594 2.108566 CTCTGCTGATGCTCCCCG 59.891 66.667 0.00 0.00 40.48 5.73
3180 3603 0.946221 GATGCTCCCCGTGCTTATCG 60.946 60.000 0.00 0.00 0.00 2.92
3185 3608 3.261951 CCCGTGCTTATCGTGCCG 61.262 66.667 0.00 0.00 0.00 5.69
3237 3660 8.689251 ACGATACCGATCTAATATCAAACATG 57.311 34.615 0.00 0.00 39.50 3.21
3238 3661 8.304596 ACGATACCGATCTAATATCAAACATGT 58.695 33.333 0.00 0.00 39.50 3.21
3242 3665 8.689251 ACCGATCTAATATCAAACATGTATCG 57.311 34.615 0.00 6.07 34.01 2.92
3243 3666 8.304596 ACCGATCTAATATCAAACATGTATCGT 58.695 33.333 15.29 5.26 32.74 3.73
3244 3667 8.799091 CCGATCTAATATCAAACATGTATCGTC 58.201 37.037 15.29 0.00 32.74 4.20
3315 3747 7.716998 TCAGAGGTTAGCCAAATGAATAATCTC 59.283 37.037 0.00 8.58 36.19 2.75
3318 3750 7.118723 AGGTTAGCCAAATGAATAATCTCACA 58.881 34.615 0.00 0.00 37.19 3.58
3320 3752 8.250332 GGTTAGCCAAATGAATAATCTCACAAA 58.750 33.333 0.00 0.00 34.09 2.83
3322 3754 7.472334 AGCCAAATGAATAATCTCACAAACT 57.528 32.000 0.00 0.00 0.00 2.66
3323 3755 7.542025 AGCCAAATGAATAATCTCACAAACTC 58.458 34.615 0.00 0.00 0.00 3.01
3335 3767 7.572523 ATCTCACAAACTCAAAGAATTCACA 57.427 32.000 8.44 0.00 0.00 3.58
3337 3769 7.250569 TCTCACAAACTCAAAGAATTCACAAC 58.749 34.615 8.44 0.00 0.00 3.32
3339 3771 7.374272 TCACAAACTCAAAGAATTCACAACAA 58.626 30.769 8.44 0.00 0.00 2.83
3342 3774 8.034215 ACAAACTCAAAGAATTCACAACAATGA 58.966 29.630 8.44 0.83 0.00 2.57
3396 3828 3.612472 GTAGAGCTCCATCTACGTCAC 57.388 52.381 10.93 0.00 41.56 3.67
3410 3842 0.790207 CGTCACGAGGAACCATGTTG 59.210 55.000 0.00 0.00 0.00 3.33
3469 3902 4.767578 AGAGTCACCTGCAACATGATAT 57.232 40.909 0.00 0.00 0.00 1.63
3484 3917 4.141642 ACATGATATGTTGCAGCCACTAGA 60.142 41.667 0.00 0.00 41.63 2.43
3489 3922 1.625315 TGTTGCAGCCACTAGACATCT 59.375 47.619 0.00 0.00 0.00 2.90
3493 3926 5.221322 TGTTGCAGCCACTAGACATCTATAG 60.221 44.000 0.00 0.00 0.00 1.31
3510 3943 9.896645 ACATCTATAGATTTAATGTATGGGCAG 57.103 33.333 12.75 0.00 31.21 4.85
3514 3947 9.167311 CTATAGATTTAATGTATGGGCAGGTTC 57.833 37.037 5.06 0.00 0.00 3.62
3534 3967 7.390440 CAGGTTCCACAAGAATTATAACAGTCA 59.610 37.037 0.00 0.00 36.69 3.41
3556 3989 6.763135 GTCATATCTCACCTACATGCTTTTCA 59.237 38.462 0.00 0.00 0.00 2.69
3558 3991 7.496920 TCATATCTCACCTACATGCTTTTCAAG 59.503 37.037 0.00 0.00 0.00 3.02
3565 3998 6.204688 CACCTACATGCTTTTCAAGTAAGTGA 59.795 38.462 0.00 0.00 40.80 3.41
3578 4011 9.528018 TTTCAAGTAAGTGAAAATTTGGCTTAG 57.472 29.630 0.00 0.00 42.94 2.18
3582 4015 8.871686 AGTAAGTGAAAATTTGGCTTAGTTTG 57.128 30.769 0.00 0.00 0.00 2.93
3584 4017 4.744631 AGTGAAAATTTGGCTTAGTTTGCG 59.255 37.500 0.00 0.00 0.00 4.85
3666 4099 3.062639 CACTACATCTCACAACAATCCGC 59.937 47.826 0.00 0.00 0.00 5.54
3669 4102 2.079158 CATCTCACAACAATCCGCAGT 58.921 47.619 0.00 0.00 0.00 4.40
3678 4111 3.194005 ACAATCCGCAGTATACTTGGG 57.806 47.619 17.09 14.27 0.00 4.12
3698 4131 0.107643 TCCACGGCATCTCACAACAA 59.892 50.000 0.00 0.00 0.00 2.83
3703 4136 1.338674 CGGCATCTCACAACAACCCTA 60.339 52.381 0.00 0.00 0.00 3.53
3740 4173 6.317140 CACTAGTTTGACCAATAGCATCACAT 59.683 38.462 0.00 0.00 0.00 3.21
3752 4185 7.174426 CCAATAGCATCACATCATTAGTGTCAT 59.826 37.037 0.00 0.00 38.16 3.06
3760 4193 5.583457 CACATCATTAGTGTCATCAAGCAGA 59.417 40.000 0.00 0.00 32.44 4.26
3761 4194 5.816258 ACATCATTAGTGTCATCAAGCAGAG 59.184 40.000 0.00 0.00 0.00 3.35
3762 4195 5.665916 TCATTAGTGTCATCAAGCAGAGA 57.334 39.130 0.00 0.00 0.00 3.10
3764 4197 2.758736 AGTGTCATCAAGCAGAGACC 57.241 50.000 0.00 0.00 0.00 3.85
3765 4198 2.255406 AGTGTCATCAAGCAGAGACCT 58.745 47.619 0.00 0.00 0.00 3.85
3766 4199 3.435275 AGTGTCATCAAGCAGAGACCTA 58.565 45.455 0.00 0.00 0.00 3.08
3767 4200 4.029520 AGTGTCATCAAGCAGAGACCTAT 58.970 43.478 0.00 0.00 0.00 2.57
3770 4203 2.968574 TCATCAAGCAGAGACCTATCCC 59.031 50.000 0.00 0.00 0.00 3.85
3771 4204 1.403814 TCAAGCAGAGACCTATCCCG 58.596 55.000 0.00 0.00 0.00 5.14
3772 4205 0.390860 CAAGCAGAGACCTATCCCGG 59.609 60.000 0.00 0.00 0.00 5.73
3773 4206 1.403687 AAGCAGAGACCTATCCCGGC 61.404 60.000 0.00 0.00 0.00 6.13
3774 4207 2.873525 GCAGAGACCTATCCCGGCC 61.874 68.421 0.00 0.00 0.00 6.13
3775 4208 2.201771 AGAGACCTATCCCGGCCC 59.798 66.667 0.00 0.00 0.00 5.80
3776 4209 2.122989 GAGACCTATCCCGGCCCA 60.123 66.667 0.00 0.00 0.00 5.36
3777 4210 1.536662 GAGACCTATCCCGGCCCAT 60.537 63.158 0.00 0.00 0.00 4.00
3778 4211 1.073706 AGACCTATCCCGGCCCATT 60.074 57.895 0.00 0.00 0.00 3.16
3779 4212 1.073199 GACCTATCCCGGCCCATTG 59.927 63.158 0.00 0.00 0.00 2.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 3.281341 TCGCAAAAATGCTCACGAATT 57.719 38.095 0.00 0.00 0.00 2.17
43 44 7.880195 TGGGAAAAAGTTCACTGATTTGAAAAA 59.120 29.630 0.00 0.00 38.08 1.94
67 68 9.656040 TGAATTTCATAAAATGTCTCCAATTGG 57.344 29.630 19.08 19.08 35.27 3.16
118 119 9.033481 TGAACATTTGAAAAATCTGATGAACAC 57.967 29.630 0.00 0.00 0.00 3.32
121 122 9.984190 TCATGAACATTTGAAAAATCTGATGAA 57.016 25.926 0.00 0.00 0.00 2.57
162 163 8.028354 TCAATGATCATTTTGAGCGTGTTTAAT 58.972 29.630 18.41 0.00 35.14 1.40
170 171 7.514573 TTGAATTCAATGATCATTTTGAGCG 57.485 32.000 18.41 6.54 35.14 5.03
381 557 7.258022 TGAATCTCAGAAAAACGTTCATTGA 57.742 32.000 0.00 3.07 0.00 2.57
388 564 9.965824 AAACATTTATGAATCTCAGAAAAACGT 57.034 25.926 1.03 0.00 40.39 3.99
438 614 8.948853 TCATAAGATGTTCACGATTTTGAAAC 57.051 30.769 0.00 0.00 37.24 2.78
449 641 6.317140 TGCTCCAGAAATCATAAGATGTTCAC 59.683 38.462 0.00 0.00 33.90 3.18
567 778 6.876789 CGCCCCAGTTTATTTATTTCCTTTTT 59.123 34.615 0.00 0.00 0.00 1.94
568 779 6.014070 ACGCCCCAGTTTATTTATTTCCTTTT 60.014 34.615 0.00 0.00 0.00 2.27
569 780 5.482526 ACGCCCCAGTTTATTTATTTCCTTT 59.517 36.000 0.00 0.00 0.00 3.11
570 781 5.020795 ACGCCCCAGTTTATTTATTTCCTT 58.979 37.500 0.00 0.00 0.00 3.36
571 782 4.606210 ACGCCCCAGTTTATTTATTTCCT 58.394 39.130 0.00 0.00 0.00 3.36
572 783 4.202080 GGACGCCCCAGTTTATTTATTTCC 60.202 45.833 0.00 0.00 34.14 3.13
573 784 4.399934 TGGACGCCCCAGTTTATTTATTTC 59.600 41.667 0.00 0.00 40.82 2.17
684 914 9.372541 CGTGTTAGTTTATACATTTCGTTGTTT 57.627 29.630 0.00 0.00 0.00 2.83
767 999 4.867047 CGGATTGATCGATGGGAAGATTAG 59.133 45.833 0.54 0.00 0.00 1.73
769 1001 3.071602 ACGGATTGATCGATGGGAAGATT 59.928 43.478 0.54 0.00 0.00 2.40
828 1060 4.177026 CAAGAACAAGAGGTAGTCGATGG 58.823 47.826 0.00 0.00 0.00 3.51
860 1092 7.213678 ACAGAACAAGGAGACAAAAACAAAAA 58.786 30.769 0.00 0.00 0.00 1.94
970 1202 4.431416 TCTCAGCTCCCAACACTAAAAA 57.569 40.909 0.00 0.00 0.00 1.94
1095 1327 0.242825 TGATGACGACGGTGAGGTTC 59.757 55.000 0.00 0.00 0.00 3.62
1164 1396 1.682740 TGGTTTCGGGTGAAAGTTCC 58.317 50.000 0.00 0.00 44.42 3.62
1168 1400 4.519540 AATTGATGGTTTCGGGTGAAAG 57.480 40.909 0.00 0.00 44.42 2.62
1223 1455 3.071479 TCGAACATGCTACAAAAGGGAC 58.929 45.455 0.00 0.00 0.00 4.46
1276 1508 7.172019 TCCTCCTGTAAATAAAACACGAGTTTC 59.828 37.037 11.41 0.00 46.79 2.78
1278 1510 6.426025 GTCCTCCTGTAAATAAAACACGAGTT 59.574 38.462 0.00 0.00 40.40 3.01
1279 1511 5.930569 GTCCTCCTGTAAATAAAACACGAGT 59.069 40.000 0.00 0.00 31.81 4.18
1289 1525 3.228453 CCGCTAGGTCCTCCTGTAAATA 58.772 50.000 0.00 0.00 44.81 1.40
1434 1670 1.066114 CGAGCTTCAGAACGTCGACC 61.066 60.000 10.58 0.00 32.32 4.79
1535 1771 0.248498 CGAGATGAAGCGCTCCGTTA 60.248 55.000 12.06 0.00 0.00 3.18
1539 1775 0.313672 AGATCGAGATGAAGCGCTCC 59.686 55.000 12.06 0.00 0.00 4.70
1540 1776 2.132740 AAGATCGAGATGAAGCGCTC 57.867 50.000 12.06 4.99 0.00 5.03
1541 1777 3.254411 TCATAAGATCGAGATGAAGCGCT 59.746 43.478 2.64 2.64 0.00 5.92
1542 1778 3.569548 TCATAAGATCGAGATGAAGCGC 58.430 45.455 0.00 0.00 0.00 5.92
1543 1779 6.550843 AGTATCATAAGATCGAGATGAAGCG 58.449 40.000 10.13 0.00 35.67 4.68
1544 1780 6.972328 GGAGTATCATAAGATCGAGATGAAGC 59.028 42.308 10.13 7.17 36.25 3.86
1578 1820 3.942748 GACGGCTTGGTTACATATGGAAA 59.057 43.478 0.72 0.00 0.00 3.13
1583 1825 3.637911 TTGGACGGCTTGGTTACATAT 57.362 42.857 0.00 0.00 0.00 1.78
1606 1862 2.368439 TGTTTCTGCAGAGCACAAAGT 58.632 42.857 22.27 0.00 33.79 2.66
1608 1864 3.708890 CATTGTTTCTGCAGAGCACAAA 58.291 40.909 31.53 21.31 34.68 2.83
1658 1914 0.752009 TCTCGACCCCATCTTCGGAG 60.752 60.000 0.00 0.00 35.89 4.63
1664 1920 0.689080 ACTGCATCTCGACCCCATCT 60.689 55.000 0.00 0.00 0.00 2.90
1670 1926 3.389206 GCGAACTGCATCTCGACC 58.611 61.111 18.69 1.69 45.45 4.79
1697 1953 7.576861 TGTGTCGAGACAATATATACCAAGA 57.423 36.000 13.72 0.00 43.77 3.02
1700 1956 5.562113 CGCTGTGTCGAGACAATATATACCA 60.562 44.000 16.86 0.00 43.77 3.25
1717 1973 3.031736 AGATAGATAACCACCGCTGTGT 58.968 45.455 7.53 0.00 41.09 3.72
1781 2125 1.517242 GTCAGCAGAAAGTGACCTGG 58.483 55.000 0.00 0.00 37.67 4.45
1846 2190 4.592192 ACGATGCGGCCCTCGATG 62.592 66.667 23.21 0.00 42.43 3.84
1867 2211 1.437573 GTGGGCGATCGATGACAGA 59.562 57.895 21.57 0.00 0.00 3.41
1912 2256 7.905604 TTTCTTGTCATTGAGTGTATCGAAT 57.094 32.000 0.00 0.00 0.00 3.34
2050 2400 5.623174 GCTCTTTAGCGTGTAGTATGTTC 57.377 43.478 0.00 0.00 39.39 3.18
2095 2445 5.008118 GGCGAAAATATGGAGAGAGGAAAAG 59.992 44.000 0.00 0.00 0.00 2.27
2099 2449 3.309296 AGGCGAAAATATGGAGAGAGGA 58.691 45.455 0.00 0.00 0.00 3.71
2100 2450 3.760580 AGGCGAAAATATGGAGAGAGG 57.239 47.619 0.00 0.00 0.00 3.69
2101 2451 6.814146 GGTAATAGGCGAAAATATGGAGAGAG 59.186 42.308 0.00 0.00 0.00 3.20
2102 2452 6.497259 AGGTAATAGGCGAAAATATGGAGAGA 59.503 38.462 0.00 0.00 0.00 3.10
2151 2502 7.565398 TCAATTAGTAAGAGCCCTCTATTCAGT 59.435 37.037 0.00 0.00 39.39 3.41
2154 2505 8.184304 TCTCAATTAGTAAGAGCCCTCTATTC 57.816 38.462 0.00 0.00 39.39 1.75
2209 2560 7.011499 TCAGTAACATACAGTTTATGGTGGT 57.989 36.000 0.00 0.00 41.64 4.16
2213 2564 8.450964 CCTGTTTCAGTAACATACAGTTTATGG 58.549 37.037 1.55 0.00 45.31 2.74
2354 2705 9.978044 TTGATGACATTTGACAAATACATTCAA 57.022 25.926 22.21 21.55 31.84 2.69
2420 2771 1.014352 AATTGATAACGCCGTGGAGC 58.986 50.000 0.00 0.00 0.00 4.70
2435 2786 6.753744 GCCTCTGCAAGTTAAATAGGAAATTG 59.246 38.462 0.00 0.00 35.52 2.32
2476 2827 4.574013 GGTACATTCTTCCAGATCAAGCAG 59.426 45.833 0.00 0.00 0.00 4.24
2533 2885 9.530129 CAGAAGAAACTACACAACGAAATATTC 57.470 33.333 0.00 0.00 0.00 1.75
2542 2894 9.447040 GGTTAAATTCAGAAGAAACTACACAAC 57.553 33.333 0.00 0.00 37.29 3.32
2617 2972 2.598565 CTGAGCCCTACATAGCAGGTA 58.401 52.381 0.00 0.00 0.00 3.08
2706 3061 1.515304 GCCAAGACGTCGCTCTCTC 60.515 63.158 10.46 0.00 0.00 3.20
2778 3133 1.528129 CCTTTCTCTCGCCTGCTTTT 58.472 50.000 0.00 0.00 0.00 2.27
2799 3154 2.545322 GCATGCGGTAGGTTCCTACTAC 60.545 54.545 22.96 16.97 38.98 2.73
2884 3242 2.158608 AGGGTGCATATTGGTCTTAGCC 60.159 50.000 0.00 0.00 0.00 3.93
2885 3243 2.880890 CAGGGTGCATATTGGTCTTAGC 59.119 50.000 0.00 0.00 0.00 3.09
2886 3244 3.117888 ACCAGGGTGCATATTGGTCTTAG 60.118 47.826 11.76 0.00 39.68 2.18
2887 3245 2.849943 ACCAGGGTGCATATTGGTCTTA 59.150 45.455 11.76 0.00 39.68 2.10
2888 3246 1.640670 ACCAGGGTGCATATTGGTCTT 59.359 47.619 11.76 0.00 39.68 3.01
2889 3247 1.298953 ACCAGGGTGCATATTGGTCT 58.701 50.000 11.76 0.00 39.68 3.85
2890 3248 2.143876 AACCAGGGTGCATATTGGTC 57.856 50.000 16.26 0.00 42.86 4.02
2891 3249 3.748645 TTAACCAGGGTGCATATTGGT 57.251 42.857 11.76 11.76 45.47 3.67
2892 3250 5.612725 AATTTAACCAGGGTGCATATTGG 57.387 39.130 10.66 10.66 36.76 3.16
2927 3289 0.179073 AATCCGGAACAGATCGGCAG 60.179 55.000 9.01 0.00 45.31 4.85
2936 3298 1.615651 CCATTGACCCAATCCGGAACA 60.616 52.381 9.01 0.00 36.56 3.18
2941 3303 0.255890 AGTCCCATTGACCCAATCCG 59.744 55.000 0.00 0.00 45.68 4.18
2942 3304 1.686115 CCAGTCCCATTGACCCAATCC 60.686 57.143 0.00 0.00 45.68 3.01
2951 3313 5.013495 AGGATGACATATACCAGTCCCATTG 59.987 44.000 0.00 0.00 33.89 2.82
3037 3409 9.968870 GAAATCACTCTAGGACGATAAAGTATT 57.031 33.333 0.00 0.00 0.00 1.89
3039 3411 7.255035 CCGAAATCACTCTAGGACGATAAAGTA 60.255 40.741 0.00 0.00 0.00 2.24
3051 3453 4.500545 CCATCAGTCCCGAAATCACTCTAG 60.501 50.000 0.00 0.00 0.00 2.43
3086 3488 1.227263 CCTAATCAGGACGTGCCCG 60.227 63.158 2.38 0.00 45.91 6.13
3092 3494 5.468540 TCATAATGACCCTAATCAGGACG 57.531 43.478 0.00 0.00 45.91 4.79
3096 3498 5.636965 CGAAGCTCATAATGACCCTAATCAG 59.363 44.000 0.00 0.00 30.46 2.90
3099 3501 4.263068 CCCGAAGCTCATAATGACCCTAAT 60.263 45.833 0.00 0.00 0.00 1.73
3101 3503 2.632996 CCCGAAGCTCATAATGACCCTA 59.367 50.000 0.00 0.00 0.00 3.53
3104 3506 2.103263 AGACCCGAAGCTCATAATGACC 59.897 50.000 0.00 0.00 0.00 4.02
3140 3542 2.484651 CAGCAGAGCAATAGCATCCATC 59.515 50.000 0.00 0.00 45.49 3.51
3141 3543 2.105993 TCAGCAGAGCAATAGCATCCAT 59.894 45.455 0.00 0.00 45.49 3.41
3144 3546 2.095668 GCATCAGCAGAGCAATAGCATC 60.096 50.000 0.00 0.00 41.72 3.91
3146 3548 1.134189 AGCATCAGCAGAGCAATAGCA 60.134 47.619 4.05 0.00 43.66 3.49
3147 3549 1.532007 GAGCATCAGCAGAGCAATAGC 59.468 52.381 4.05 0.00 45.49 2.97
3148 3550 2.144730 GGAGCATCAGCAGAGCAATAG 58.855 52.381 4.05 0.00 45.49 1.73
3149 3551 1.202734 GGGAGCATCAGCAGAGCAATA 60.203 52.381 4.05 0.00 45.49 1.90
3151 3553 1.077930 GGGAGCATCAGCAGAGCAA 60.078 57.895 4.05 0.00 45.49 3.91
3152 3554 2.588439 GGGAGCATCAGCAGAGCA 59.412 61.111 4.05 0.00 45.49 4.26
3185 3608 2.031163 CGATTCGATCCAGGGGCC 59.969 66.667 0.00 0.00 0.00 5.80
3237 3660 7.027760 TCTAGATTATTGCGATTGGACGATAC 58.972 38.462 0.00 0.00 35.09 2.24
3238 3661 7.153217 TCTAGATTATTGCGATTGGACGATA 57.847 36.000 0.00 0.00 35.09 2.92
3241 3664 6.712241 ATTCTAGATTATTGCGATTGGACG 57.288 37.500 0.00 0.00 0.00 4.79
3242 3665 9.813080 GTTAATTCTAGATTATTGCGATTGGAC 57.187 33.333 0.00 0.00 0.00 4.02
3243 3666 9.554395 TGTTAATTCTAGATTATTGCGATTGGA 57.446 29.630 0.00 0.00 0.00 3.53
3315 3747 7.579589 TTGTTGTGAATTCTTTGAGTTTGTG 57.420 32.000 7.05 0.00 0.00 3.33
3318 3750 9.434420 TTTCATTGTTGTGAATTCTTTGAGTTT 57.566 25.926 7.05 0.00 37.88 2.66
3320 3752 8.872845 GTTTTCATTGTTGTGAATTCTTTGAGT 58.127 29.630 7.05 0.00 37.88 3.41
3322 3754 8.768957 TGTTTTCATTGTTGTGAATTCTTTGA 57.231 26.923 7.05 0.00 37.88 2.69
3329 3761 8.659925 TTGCTTATGTTTTCATTGTTGTGAAT 57.340 26.923 0.00 0.00 41.25 2.57
3335 3767 9.995003 TTAGGATTTGCTTATGTTTTCATTGTT 57.005 25.926 0.00 0.00 41.25 2.83
3373 3805 2.950309 GACGTAGATGGAGCTCTACCAA 59.050 50.000 14.64 0.00 43.05 3.67
3393 3825 1.691976 ACTCAACATGGTTCCTCGTGA 59.308 47.619 0.00 0.00 0.00 4.35
3396 3828 1.001974 TCCACTCAACATGGTTCCTCG 59.998 52.381 0.00 0.00 38.47 4.63
3410 3842 1.878522 CGGCTACGTGCATCCACTC 60.879 63.158 0.00 0.00 45.15 3.51
3432 3864 3.752222 TGACTCTTCGAGGAGTGACTTAC 59.248 47.826 32.04 17.68 45.32 2.34
3433 3865 3.752222 GTGACTCTTCGAGGAGTGACTTA 59.248 47.826 30.57 13.16 45.32 2.24
3469 3902 1.625315 AGATGTCTAGTGGCTGCAACA 59.375 47.619 10.27 0.27 0.00 3.33
3484 3917 9.896645 CTGCCCATACATTAAATCTATAGATGT 57.103 33.333 16.01 13.07 34.49 3.06
3489 3922 8.107095 GGAACCTGCCCATACATTAAATCTATA 58.893 37.037 0.00 0.00 0.00 1.31
3493 3926 4.892934 TGGAACCTGCCCATACATTAAATC 59.107 41.667 0.00 0.00 0.00 2.17
3510 3943 7.681939 TGACTGTTATAATTCTTGTGGAACC 57.318 36.000 0.00 0.00 36.70 3.62
3534 3967 7.798596 CTTGAAAAGCATGTAGGTGAGATAT 57.201 36.000 0.00 0.00 36.98 1.63
3556 3989 9.313118 CAAACTAAGCCAAATTTTCACTTACTT 57.687 29.630 0.00 0.00 0.00 2.24
3558 3991 7.564128 GCAAACTAAGCCAAATTTTCACTTAC 58.436 34.615 0.00 0.00 0.00 2.34
3565 3998 6.292649 GCTTTACGCAAACTAAGCCAAATTTT 60.293 34.615 0.00 0.00 37.59 1.82
3576 4009 6.470557 AAAACTATCGCTTTACGCAAACTA 57.529 33.333 0.00 0.00 43.23 2.24
3577 4010 5.352643 AAAACTATCGCTTTACGCAAACT 57.647 34.783 0.00 0.00 43.23 2.66
3578 4011 7.899330 TGTATAAAACTATCGCTTTACGCAAAC 59.101 33.333 0.00 0.00 43.23 2.93
3582 4015 8.485591 AGATTGTATAAAACTATCGCTTTACGC 58.514 33.333 0.00 0.00 42.86 4.42
3666 4099 1.472728 GCCGTGGACCCAAGTATACTG 60.473 57.143 6.06 0.94 0.00 2.74
3669 4102 1.414919 GATGCCGTGGACCCAAGTATA 59.585 52.381 1.60 0.00 0.00 1.47
3678 4111 0.602638 TGTTGTGAGATGCCGTGGAC 60.603 55.000 0.00 0.00 0.00 4.02
3698 4131 1.080666 AGTGGGCTAAAGGTCTAGGGT 59.919 52.381 0.00 0.00 0.00 4.34
3703 4136 3.908103 TCAAACTAGTGGGCTAAAGGTCT 59.092 43.478 0.00 0.00 0.00 3.85
3740 4173 5.414360 GTCTCTGCTTGATGACACTAATGA 58.586 41.667 0.00 0.00 0.00 2.57
3752 4185 1.403814 CGGGATAGGTCTCTGCTTGA 58.596 55.000 0.00 0.00 0.00 3.02
3760 4193 1.073706 AATGGGCCGGGATAGGTCT 60.074 57.895 2.18 0.00 35.87 3.85
3761 4194 1.073199 CAATGGGCCGGGATAGGTC 59.927 63.158 2.18 0.00 34.51 3.85
3762 4195 3.250847 CAATGGGCCGGGATAGGT 58.749 61.111 2.18 0.00 0.00 3.08


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

AutoCloner maintained by Alex Coulton.