Multiple sequence alignment - TraesCS2B01G296100

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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 TraesCS2B01G296100 chr2B 100.000 4339 0 0 1 4339 413061237 413065575 0.000000e+00 8013.0
1 TraesCS2B01G296100 chr2D 92.120 2944 125 31 800 3691 347807039 347809927 0.000000e+00 4052.0
2 TraesCS2B01G296100 chr2D 90.737 475 19 13 89 546 347805851 347806317 1.030000e-170 610.0
3 TraesCS2B01G296100 chr2D 95.417 240 9 2 562 801 347806566 347806803 8.810000e-102 381.0
4 TraesCS2B01G296100 chr2D 97.826 46 0 1 3734 3779 347809925 347809969 1.290000e-10 78.7
5 TraesCS2B01G296100 chr2D 81.905 105 6 5 4015 4119 347810194 347810285 4.650000e-10 76.8
6 TraesCS2B01G296100 chr2A 94.758 1946 71 10 461 2386 461414227 461416161 0.000000e+00 3000.0
7 TraesCS2B01G296100 chr2A 93.537 1408 63 11 2404 3799 461416428 461417819 0.000000e+00 2071.0
8 TraesCS2B01G296100 chr2A 92.593 378 12 9 14 390 461411144 461411506 2.970000e-146 529.0
9 TraesCS2B01G296100 chr2A 87.124 233 15 1 4122 4339 461421477 461421709 2.590000e-62 250.0
10 TraesCS2B01G296100 chr2A 95.238 42 2 0 4074 4115 461420269 461420310 2.800000e-07 67.6
11 TraesCS2B01G296100 chr5A 82.751 3177 326 100 563 3615 569225212 569222134 0.000000e+00 2627.0
12 TraesCS2B01G296100 chr5A 84.604 2663 259 64 1167 3726 569219726 569217112 0.000000e+00 2507.0
13 TraesCS2B01G296100 chr5A 85.135 2415 254 46 1106 3457 569183920 569181548 0.000000e+00 2374.0
14 TraesCS2B01G296100 chr5A 84.438 2339 243 61 1167 3433 569151752 569154041 0.000000e+00 2191.0
15 TraesCS2B01G296100 chr5A 96.970 33 1 0 243 275 569225590 569225558 6.060000e-04 56.5
16 TraesCS2B01G296100 chr5D 83.128 2928 303 82 698 3530 449936543 449933712 0.000000e+00 2494.0
17 TraesCS2B01G296100 chr5D 85.932 2168 187 67 563 2684 449941457 449939362 0.000000e+00 2206.0
18 TraesCS2B01G296100 chr5D 82.329 747 89 21 2742 3457 449981570 449980836 3.710000e-170 608.0
19 TraesCS2B01G296100 chr5D 83.505 679 77 17 2065 2736 449886430 449887080 6.210000e-168 601.0
20 TraesCS2B01G296100 chr5D 82.720 706 80 20 2748 3423 449939254 449938561 1.340000e-164 590.0
21 TraesCS2B01G296100 chr5D 79.809 629 63 32 2749 3355 449887123 449887709 2.430000e-107 399.0
22 TraesCS2B01G296100 chr5D 86.842 114 5 5 3623 3726 449933651 449933538 7.620000e-23 119.0
23 TraesCS2B01G296100 chr5D 78.673 211 19 16 392 585 449983961 449983760 2.740000e-22 117.0
24 TraesCS2B01G296100 chr5B 82.452 3026 303 97 847 3726 549949424 549946481 0.000000e+00 2436.0
25 TraesCS2B01G296100 chr5B 84.877 1382 119 43 710 2047 549954528 549953193 0.000000e+00 1312.0
26 TraesCS2B01G296100 chr5B 82.394 1579 181 57 2071 3591 549953067 549951528 0.000000e+00 1286.0
27 TraesCS2B01G296100 chr5B 86.182 1129 98 30 1028 2125 549711102 549712203 0.000000e+00 1168.0
28 TraesCS2B01G296100 chr5B 81.490 443 60 11 2295 2736 549712198 549712619 1.160000e-90 344.0
29 TraesCS2B01G296100 chr5B 82.051 78 3 3 203 275 549955075 549955004 6.060000e-04 56.5
30 TraesCS2B01G296100 chr7B 79.813 748 128 15 1483 2216 733750700 733751438 1.380000e-144 523.0
31 TraesCS2B01G296100 chr7B 79.521 752 133 16 1478 2216 733788266 733789009 2.310000e-142 516.0
32 TraesCS2B01G296100 chr7B 85.897 234 27 1 1140 1373 733359539 733359312 1.210000e-60 244.0
33 TraesCS2B01G296100 chr7B 85.043 234 29 1 1140 1373 733750376 733750603 2.610000e-57 233.0
34 TraesCS2B01G296100 chr7D 84.615 234 30 1 1140 1373 630327979 630327752 1.210000e-55 228.0
35 TraesCS2B01G296100 chr7A 84.188 234 31 1 1140 1373 726859520 726859293 5.650000e-54 222.0


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 TraesCS2B01G296100 chr2B 413061237 413065575 4338 False 8013.000000 8013 100.000000 1 4339 1 chr2B.!!$F1 4338
1 TraesCS2B01G296100 chr2D 347805851 347810285 4434 False 1039.700000 4052 91.601000 89 4119 5 chr2D.!!$F1 4030
2 TraesCS2B01G296100 chr2A 461411144 461421709 10565 False 1183.520000 3000 92.650000 14 4339 5 chr2A.!!$F1 4325
3 TraesCS2B01G296100 chr5A 569181548 569183920 2372 True 2374.000000 2374 85.135000 1106 3457 1 chr5A.!!$R1 2351
4 TraesCS2B01G296100 chr5A 569151752 569154041 2289 False 2191.000000 2191 84.438000 1167 3433 1 chr5A.!!$F1 2266
5 TraesCS2B01G296100 chr5A 569217112 569225590 8478 True 1730.166667 2627 88.108333 243 3726 3 chr5A.!!$R2 3483
6 TraesCS2B01G296100 chr5D 449933538 449941457 7919 True 1352.250000 2494 84.655500 563 3726 4 chr5D.!!$R1 3163
7 TraesCS2B01G296100 chr5D 449886430 449887709 1279 False 500.000000 601 81.657000 2065 3355 2 chr5D.!!$F1 1290
8 TraesCS2B01G296100 chr5D 449980836 449983961 3125 True 362.500000 608 80.501000 392 3457 2 chr5D.!!$R2 3065
9 TraesCS2B01G296100 chr5B 549946481 549955075 8594 True 1272.625000 2436 82.943500 203 3726 4 chr5B.!!$R1 3523
10 TraesCS2B01G296100 chr5B 549711102 549712619 1517 False 756.000000 1168 83.836000 1028 2736 2 chr5B.!!$F1 1708
11 TraesCS2B01G296100 chr7B 733788266 733789009 743 False 516.000000 516 79.521000 1478 2216 1 chr7B.!!$F1 738
12 TraesCS2B01G296100 chr7B 733750376 733751438 1062 False 378.000000 523 82.428000 1140 2216 2 chr7B.!!$F2 1076

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
987 4483 0.035317 TTTGTCATCGACTGCAGGCT 59.965 50.0 19.55 0.0 33.15 4.58 F
1911 5454 0.615331 TGTGTCAATCCTGGCTCTCC 59.385 55.0 0.00 0.0 0.00 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2439 6392 0.038892 GCTCGTTTGAGACACGGGTA 60.039 55.0 0.0 0.0 45.57 3.69 R
3871 13226 0.112412 AGAAAACATCCGGCAACCCT 59.888 50.0 0.0 0.0 0.00 4.34 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
61 62 7.201565 GGCTACAGTTTGTATTCATCTCTGTTC 60.202 40.741 0.00 0.00 36.36 3.18
75 76 9.730705 TTCATCTCTGTTCTATTTGAAACTCAT 57.269 29.630 0.00 0.00 36.30 2.90
76 77 9.376075 TCATCTCTGTTCTATTTGAAACTCATC 57.624 33.333 0.00 0.00 36.30 2.92
77 78 9.159364 CATCTCTGTTCTATTTGAAACTCATCA 57.841 33.333 0.00 0.00 36.30 3.07
78 79 8.768957 TCTCTGTTCTATTTGAAACTCATCAG 57.231 34.615 0.00 0.00 36.30 2.90
79 80 7.821359 TCTCTGTTCTATTTGAAACTCATCAGG 59.179 37.037 0.00 0.00 36.30 3.86
80 81 6.372659 TCTGTTCTATTTGAAACTCATCAGGC 59.627 38.462 0.00 0.00 36.30 4.85
81 82 6.240894 TGTTCTATTTGAAACTCATCAGGCT 58.759 36.000 0.00 0.00 36.30 4.58
82 83 6.149973 TGTTCTATTTGAAACTCATCAGGCTG 59.850 38.462 8.58 8.58 36.30 4.85
83 84 3.863142 ATTTGAAACTCATCAGGCTGC 57.137 42.857 10.34 0.00 0.00 5.25
84 85 1.159285 TTGAAACTCATCAGGCTGCG 58.841 50.000 10.34 3.30 0.00 5.18
85 86 0.674581 TGAAACTCATCAGGCTGCGG 60.675 55.000 10.34 4.14 0.00 5.69
86 87 0.391661 GAAACTCATCAGGCTGCGGA 60.392 55.000 10.34 8.64 0.00 5.54
87 88 0.392193 AAACTCATCAGGCTGCGGAG 60.392 55.000 24.46 24.46 0.00 4.63
124 125 2.876550 GGCGTACAAAAGTCTTGGAGTT 59.123 45.455 0.00 0.00 0.00 3.01
128 129 1.676006 ACAAAAGTCTTGGAGTTGCGG 59.324 47.619 0.00 0.00 0.00 5.69
151 153 4.929707 CCGCTCCGTAATGGGCCC 62.930 72.222 17.59 17.59 38.76 5.80
172 174 3.054434 CCAATAGGACACCACTCCATCAA 60.054 47.826 0.00 0.00 36.89 2.57
232 237 1.375326 GCCGGGGACAACTTCTTCT 59.625 57.895 2.18 0.00 0.00 2.85
233 238 0.250770 GCCGGGGACAACTTCTTCTT 60.251 55.000 2.18 0.00 0.00 2.52
234 239 1.809684 CCGGGGACAACTTCTTCTTC 58.190 55.000 0.00 0.00 0.00 2.87
308 314 0.108281 GGTTCTAGTCCACGCCCTTC 60.108 60.000 0.00 0.00 0.00 3.46
349 356 2.288395 CGCAGAGGTTTGCCAGAATTTT 60.288 45.455 0.00 0.00 41.01 1.82
371 378 5.336150 TCTCTTGGATGTCTCATGAGTTC 57.664 43.478 21.92 16.07 37.54 3.01
383 390 3.059884 TCATGAGTTCGCTCTTTGTGTC 58.940 45.455 0.00 0.00 44.38 3.67
390 397 3.026630 TCGCTCTTTGTGTCGATTTCT 57.973 42.857 0.00 0.00 0.00 2.52
473 3157 0.106918 TGCCAGAAAACCTGTTCCGT 60.107 50.000 0.00 0.00 41.33 4.69
522 3413 9.784531 ATTCTGAATCTCGTATGAATAAACCAT 57.215 29.630 0.00 0.00 0.00 3.55
630 3773 0.535335 GCACGTCAGGGGTCAGATAA 59.465 55.000 0.00 0.00 0.00 1.75
730 3902 5.514274 TTGTAGCTTTCCAACCTTTTGAG 57.486 39.130 0.00 0.00 34.24 3.02
778 4012 1.203052 CATGTGCTGTTGATTGTCCCC 59.797 52.381 0.00 0.00 0.00 4.81
795 4034 1.470098 CCCCTTCAATCTTTGCTCGTG 59.530 52.381 0.00 0.00 0.00 4.35
885 4376 2.724977 TACTCCACTTGACTCAAGCG 57.275 50.000 17.29 8.99 44.43 4.68
987 4483 0.035317 TTTGTCATCGACTGCAGGCT 59.965 50.000 19.55 0.00 33.15 4.58
1019 4518 8.687292 ATACTGATGAGGTTGATTAGTACGTA 57.313 34.615 0.00 0.00 28.04 3.57
1023 4522 7.923888 TGATGAGGTTGATTAGTACGTACTAC 58.076 38.462 30.26 21.99 38.43 2.73
1083 4585 5.305585 CCTCACTTCACTTGCTAAAACCTA 58.694 41.667 0.00 0.00 0.00 3.08
1084 4586 5.179555 CCTCACTTCACTTGCTAAAACCTAC 59.820 44.000 0.00 0.00 0.00 3.18
1085 4587 5.676552 TCACTTCACTTGCTAAAACCTACA 58.323 37.500 0.00 0.00 0.00 2.74
1086 4588 5.758296 TCACTTCACTTGCTAAAACCTACAG 59.242 40.000 0.00 0.00 0.00 2.74
1087 4589 5.527582 CACTTCACTTGCTAAAACCTACAGT 59.472 40.000 0.00 0.00 0.00 3.55
1088 4590 6.704493 CACTTCACTTGCTAAAACCTACAGTA 59.296 38.462 0.00 0.00 0.00 2.74
1089 4591 6.704937 ACTTCACTTGCTAAAACCTACAGTAC 59.295 38.462 0.00 0.00 0.00 2.73
1090 4592 5.544650 TCACTTGCTAAAACCTACAGTACC 58.455 41.667 0.00 0.00 0.00 3.34
1401 4928 6.038936 TGTTATGTCAATTCATCTCCTGCATG 59.961 38.462 0.00 0.00 0.00 4.06
1508 5051 0.882042 CGAGCAGCTTGGACACACTT 60.882 55.000 0.94 0.00 0.00 3.16
1784 5327 4.899239 CCGGTGATGGCGAGCTCC 62.899 72.222 8.47 0.47 0.00 4.70
1911 5454 0.615331 TGTGTCAATCCTGGCTCTCC 59.385 55.000 0.00 0.00 0.00 3.71
1960 5503 0.987294 ACATGGACAGGGGTCTCAAG 59.013 55.000 0.00 0.00 43.77 3.02
2075 5734 6.038603 TCAGATTATTTGCATTGCAGGTAGAC 59.961 38.462 11.76 4.46 40.61 2.59
2076 5735 4.981806 TTATTTGCATTGCAGGTAGACC 57.018 40.909 11.76 0.00 40.61 3.85
2162 5844 1.744741 GAGCTGCTGGTGCTTCTCC 60.745 63.158 7.01 0.00 41.30 3.71
2223 5905 1.002430 GTCCATCAGGTGAGTTGCAGA 59.998 52.381 0.00 0.00 35.89 4.26
2249 5932 6.713762 TTTCATGGAGTGTTTCACATTCTT 57.286 33.333 0.00 0.00 35.48 2.52
2281 5964 2.036733 TCTGACGGGAAATGTCGAACTT 59.963 45.455 0.00 0.00 39.22 2.66
2357 6045 3.492829 GCAGCCATAAGGTACTACCACTC 60.493 52.174 8.01 0.00 41.95 3.51
2439 6392 7.817478 TGAAATCGTGTATCTTGTGATTGTAGT 59.183 33.333 0.00 0.00 34.32 2.73
2505 6458 1.135373 CGTCTGGCTACTCGTGTGATT 60.135 52.381 0.00 0.00 0.00 2.57
2574 6527 1.152963 GGTGCGCAATCTATGGGGT 60.153 57.895 14.00 0.00 42.02 4.95
2580 6533 1.812571 CGCAATCTATGGGGTTATGCC 59.187 52.381 0.00 0.00 38.28 4.40
2647 6600 2.030717 CCTATTCTCTCCGTGTCCATCG 60.031 54.545 0.00 0.00 0.00 3.84
2736 6708 4.245660 TGCAGACTAGTTCCTGAATTTCG 58.754 43.478 14.18 0.00 32.37 3.46
2762 6774 6.826668 TCAACTTTAGTCCATCTTCTTGTGA 58.173 36.000 0.00 0.00 0.00 3.58
2765 6777 2.777832 AGTCCATCTTCTTGTGAGGC 57.222 50.000 0.00 0.00 0.00 4.70
2775 6800 2.358957 TCTTGTGAGGCATCATTTCGG 58.641 47.619 3.55 0.00 37.87 4.30
2805 6831 5.532557 TCAATATGTAGCATCTCGGTGAAG 58.467 41.667 0.00 0.00 0.00 3.02
2814 6840 3.380637 GCATCTCGGTGAAGGTTACTCTA 59.619 47.826 0.00 0.00 0.00 2.43
3029 7087 2.772287 AGTTCCAGCTTCACTTGTAGC 58.228 47.619 0.00 0.00 38.51 3.58
3170 7240 4.037927 CCAACTGGGATAAAGAGGTAGGA 58.962 47.826 0.00 0.00 40.01 2.94
3190 7260 8.394877 GGTAGGAAAATTTCAAACCAAAACTTG 58.605 33.333 18.14 0.00 36.53 3.16
3205 7277 1.954146 CTTGTACCACGCACACGCT 60.954 57.895 0.00 0.00 45.53 5.07
3322 7406 1.118965 TTCAGTTCGTCCCTGCCTCA 61.119 55.000 0.00 0.00 0.00 3.86
3409 12696 3.893813 GCTGGGCAAATGAGATAAGGAAT 59.106 43.478 0.00 0.00 0.00 3.01
3433 12724 2.418976 GTCAGGAATTTGGTTACCGCTC 59.581 50.000 0.00 0.00 0.00 5.03
3493 12791 2.027625 GAAGCGTCACCCAACGAGG 61.028 63.158 0.00 0.00 45.37 4.63
3518 12817 6.868339 GGATCTGTTTTGGTGATTTTTGTAGG 59.132 38.462 0.00 0.00 0.00 3.18
3557 12868 3.198635 TGGGATGTTTTCACAGGCAAAAA 59.801 39.130 0.00 0.00 35.94 1.94
3728 13063 5.291178 TGCTGATGTGGAAAAACTGAAATG 58.709 37.500 0.00 0.00 0.00 2.32
3799 13134 3.626670 CGGTGTGTGTACCAAGGTAAAAA 59.373 43.478 0.00 0.00 40.89 1.94
3846 13201 1.155424 TTGCTGACGAACGGACAACC 61.155 55.000 0.00 0.00 0.00 3.77
3862 13217 3.525221 CCAACCAATGGCCGGATC 58.475 61.111 5.05 0.00 43.80 3.36
3863 13218 2.480610 CCAACCAATGGCCGGATCG 61.481 63.158 5.05 0.00 43.80 3.69
3864 13219 1.451207 CAACCAATGGCCGGATCGA 60.451 57.895 5.05 0.00 0.00 3.59
3865 13220 1.029408 CAACCAATGGCCGGATCGAA 61.029 55.000 5.05 0.00 0.00 3.71
3866 13221 0.322997 AACCAATGGCCGGATCGAAA 60.323 50.000 5.05 0.00 0.00 3.46
3867 13222 1.029947 ACCAATGGCCGGATCGAAAC 61.030 55.000 5.05 0.00 0.00 2.78
3868 13223 1.029408 CCAATGGCCGGATCGAAACA 61.029 55.000 5.05 0.00 0.00 2.83
3869 13224 0.098728 CAATGGCCGGATCGAAACAC 59.901 55.000 5.05 0.00 0.00 3.32
3870 13225 1.029947 AATGGCCGGATCGAAACACC 61.030 55.000 5.05 0.00 0.00 4.16
3871 13226 2.046700 GGCCGGATCGAAACACCA 60.047 61.111 5.05 0.00 0.00 4.17
3872 13227 2.106683 GGCCGGATCGAAACACCAG 61.107 63.158 5.05 0.00 0.00 4.00
3873 13228 2.106683 GCCGGATCGAAACACCAGG 61.107 63.158 5.05 0.00 0.00 4.45
3874 13229 1.449601 CCGGATCGAAACACCAGGG 60.450 63.158 0.00 0.00 0.00 4.45
3875 13230 1.295423 CGGATCGAAACACCAGGGT 59.705 57.895 0.00 0.00 0.00 4.34
3876 13231 0.321298 CGGATCGAAACACCAGGGTT 60.321 55.000 0.00 0.00 0.00 4.11
3877 13232 1.165270 GGATCGAAACACCAGGGTTG 58.835 55.000 0.00 0.00 0.00 3.77
3878 13233 0.521735 GATCGAAACACCAGGGTTGC 59.478 55.000 0.00 0.00 0.00 4.17
3879 13234 0.893727 ATCGAAACACCAGGGTTGCC 60.894 55.000 0.00 0.00 0.00 4.52
3880 13235 2.903547 CGAAACACCAGGGTTGCCG 61.904 63.158 0.00 0.00 0.00 5.69
3881 13236 2.520741 AAACACCAGGGTTGCCGG 60.521 61.111 0.00 0.00 0.00 6.13
3882 13237 2.969300 GAAACACCAGGGTTGCCGGA 62.969 60.000 5.05 0.00 0.00 5.14
3883 13238 2.366153 AAACACCAGGGTTGCCGGAT 62.366 55.000 5.05 0.00 0.00 4.18
3884 13239 2.751436 CACCAGGGTTGCCGGATG 60.751 66.667 5.05 0.00 0.00 3.51
3885 13240 3.256960 ACCAGGGTTGCCGGATGT 61.257 61.111 5.05 0.00 0.00 3.06
3886 13241 2.035626 CCAGGGTTGCCGGATGTT 59.964 61.111 5.05 0.00 0.00 2.71
3887 13242 1.606313 CCAGGGTTGCCGGATGTTT 60.606 57.895 5.05 0.00 0.00 2.83
3888 13243 1.184970 CCAGGGTTGCCGGATGTTTT 61.185 55.000 5.05 0.00 0.00 2.43
3889 13244 0.243636 CAGGGTTGCCGGATGTTTTC 59.756 55.000 5.05 0.00 0.00 2.29
3890 13245 0.112412 AGGGTTGCCGGATGTTTTCT 59.888 50.000 5.05 0.00 0.00 2.52
3891 13246 0.966179 GGGTTGCCGGATGTTTTCTT 59.034 50.000 5.05 0.00 0.00 2.52
3892 13247 1.067846 GGGTTGCCGGATGTTTTCTTC 60.068 52.381 5.05 0.00 0.00 2.87
3893 13248 1.401018 GGTTGCCGGATGTTTTCTTCG 60.401 52.381 5.05 0.00 0.00 3.79
3942 13346 3.359523 GAACCGCCCCCACGTTTC 61.360 66.667 0.00 0.00 0.00 2.78
3977 13381 2.579787 CGTCGACCTGTCCATCGC 60.580 66.667 10.58 0.00 38.24 4.58
3978 13382 2.202756 GTCGACCTGTCCATCGCC 60.203 66.667 3.51 0.00 38.24 5.54
3979 13383 3.822192 TCGACCTGTCCATCGCCG 61.822 66.667 0.00 0.00 38.24 6.46
4001 13421 1.003355 CCCGTCAACACATGGCTCT 60.003 57.895 0.00 0.00 0.00 4.09
4002 13422 0.249120 CCCGTCAACACATGGCTCTA 59.751 55.000 0.00 0.00 0.00 2.43
4003 13423 1.645034 CCGTCAACACATGGCTCTAG 58.355 55.000 0.00 0.00 0.00 2.43
4005 13425 1.672737 CGTCAACACATGGCTCTAGCA 60.673 52.381 4.07 0.00 44.36 3.49
4006 13426 2.005451 GTCAACACATGGCTCTAGCAG 58.995 52.381 4.07 0.00 44.36 4.24
4051 13510 2.434331 GCACCCTGCACCCTAACA 59.566 61.111 0.00 0.00 44.26 2.41
4055 13514 1.559682 CACCCTGCACCCTAACATACT 59.440 52.381 0.00 0.00 0.00 2.12
4069 15779 1.062886 ACATACTCAGGGCTGCCTCTA 60.063 52.381 19.68 2.95 0.00 2.43
4070 15780 2.042464 CATACTCAGGGCTGCCTCTAA 58.958 52.381 19.68 0.00 0.00 2.10
4071 15781 1.486211 TACTCAGGGCTGCCTCTAAC 58.514 55.000 19.68 0.61 0.00 2.34
4119 15848 1.743772 GCCTCCGCAGAAGCTAAATGA 60.744 52.381 0.00 0.00 39.10 2.57
4120 15849 2.843701 CCTCCGCAGAAGCTAAATGAT 58.156 47.619 0.00 0.00 39.10 2.45
4186 17090 8.976986 AAATTTAGTTGAATCATCAAGCAGAC 57.023 30.769 0.00 0.00 45.88 3.51
4205 17109 0.729116 CGAATGCAGGACCATCACAC 59.271 55.000 0.00 0.00 0.00 3.82
4226 17130 0.895100 TAGCAGCAAAGGCACCCAAG 60.895 55.000 0.00 0.00 44.61 3.61
4252 17156 3.598019 ATATGCTTGTTTGGTTGCCTG 57.402 42.857 0.00 0.00 0.00 4.85
4254 17158 1.950630 GCTTGTTTGGTTGCCTGCG 60.951 57.895 0.00 0.00 0.00 5.18
4285 17189 3.396560 CTCCAGCTTGCATCATATCGAA 58.603 45.455 0.00 0.00 0.00 3.71
4290 17194 4.093115 CAGCTTGCATCATATCGAAGATCC 59.907 45.833 0.00 0.00 45.12 3.36
4292 17196 4.329528 GCTTGCATCATATCGAAGATCCTC 59.670 45.833 0.00 0.00 45.12 3.71
4293 17197 4.102035 TGCATCATATCGAAGATCCTCG 57.898 45.455 7.42 7.42 45.12 4.63
4329 17233 8.515414 GCCTAGTTGAACAGATGTAAAGATTTT 58.485 33.333 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 1.791103 TTCCAAGGCGAAAACTGGCG 61.791 55.000 0.00 0.00 36.92 5.69
9 10 0.387565 TTTCCAAGGCGAAAACTGGC 59.612 50.000 0.00 0.00 0.00 4.85
10 11 2.863740 GTTTTTCCAAGGCGAAAACTGG 59.136 45.455 16.51 0.00 40.51 4.00
11 12 2.533942 CGTTTTTCCAAGGCGAAAACTG 59.466 45.455 19.12 13.07 40.51 3.16
12 13 2.424246 TCGTTTTTCCAAGGCGAAAACT 59.576 40.909 19.12 0.00 40.51 2.66
61 62 4.495349 CGCAGCCTGATGAGTTTCAAATAG 60.495 45.833 0.00 0.00 0.00 1.73
128 129 2.125269 ATTACGGAGCGGGTGCAC 60.125 61.111 8.80 8.80 46.23 4.57
151 153 3.912496 TGATGGAGTGGTGTCCTATTG 57.088 47.619 0.00 0.00 37.52 1.90
232 237 2.754375 GGACGAAGGCCCCAAGAA 59.246 61.111 0.00 0.00 0.00 2.52
233 238 3.327404 GGGACGAAGGCCCCAAGA 61.327 66.667 0.00 0.00 42.73 3.02
281 286 1.063166 GGACTAGAACCGTACCGCG 59.937 63.158 0.00 0.00 40.95 6.46
295 301 3.322466 CAGGGAAGGGCGTGGACT 61.322 66.667 0.00 0.00 0.00 3.85
308 314 2.357009 CGATGGAGCAAAAAGATCAGGG 59.643 50.000 0.00 0.00 33.23 4.45
349 356 4.142293 CGAACTCATGAGACATCCAAGAGA 60.142 45.833 29.27 0.00 0.00 3.10
371 378 3.423645 GGAAGAAATCGACACAAAGAGCG 60.424 47.826 0.00 0.00 0.00 5.03
383 390 5.613142 GCAACAGCAAATTTGGAAGAAATCG 60.613 40.000 19.47 0.88 0.00 3.34
390 397 1.487976 TGGGCAACAGCAAATTTGGAA 59.512 42.857 19.47 0.00 39.74 3.53
473 3157 5.378332 TGGGTTCCTGAATTTCGAGTTAAA 58.622 37.500 0.00 0.00 0.00 1.52
522 3413 0.698198 TCAGTTAACCACCCACCCCA 60.698 55.000 0.88 0.00 0.00 4.96
630 3773 1.066858 GTCGTCAGGGTCATGTGTCAT 60.067 52.381 0.00 0.00 0.00 3.06
730 3902 2.658224 CGGCGCGTTTGCACTATTATAC 60.658 50.000 8.43 0.00 42.97 1.47
778 4012 5.809562 ACTATCTCACGAGCAAAGATTGAAG 59.190 40.000 0.00 0.00 32.25 3.02
885 4376 1.266718 TGAACCAGTCAATTTCAGCGC 59.733 47.619 0.00 0.00 31.51 5.92
939 4434 2.246327 AGGAAACCAAGGGGAAACAGAA 59.754 45.455 0.00 0.00 38.05 3.02
1083 4585 2.368875 CCTGTGAAGAAGGTGGTACTGT 59.631 50.000 0.00 0.00 0.00 3.55
1084 4586 2.368875 ACCTGTGAAGAAGGTGGTACTG 59.631 50.000 0.00 0.00 46.51 2.74
1085 4587 2.690840 ACCTGTGAAGAAGGTGGTACT 58.309 47.619 0.00 0.00 46.51 2.73
1401 4928 6.331369 TGTTCATTCAGGAGGATCAAAAAC 57.669 37.500 0.00 0.00 36.25 2.43
1508 5051 2.597217 CCGAAGGCTTGCCCACAA 60.597 61.111 3.46 0.00 46.14 3.33
1911 5454 1.070445 GGATGGAGAGAGCCTGATGTG 59.930 57.143 0.00 0.00 0.00 3.21
1943 5486 0.916358 CCCTTGAGACCCCTGTCCAT 60.916 60.000 0.00 0.00 42.81 3.41
2075 5734 5.012239 TCAGAAGATGGACCATGAAAAAGG 58.988 41.667 12.99 0.00 0.00 3.11
2076 5735 5.709164 AGTCAGAAGATGGACCATGAAAAAG 59.291 40.000 12.99 0.00 34.58 2.27
2162 5844 0.107165 GGATTTGGGAGAAGTCCGGG 60.107 60.000 0.00 0.00 45.05 5.73
2249 5932 1.228124 CCGTCAGAAAGGGGCACAA 60.228 57.895 0.00 0.00 0.00 3.33
2257 5940 2.683968 TCGACATTTCCCGTCAGAAAG 58.316 47.619 0.00 0.00 39.04 2.62
2281 5964 2.930950 ACCTGTGTTTAAGCTGCAAGA 58.069 42.857 1.02 0.00 34.07 3.02
2357 6045 6.377327 AAAGGTTATGAGTCTGTGTTGTTG 57.623 37.500 0.00 0.00 0.00 3.33
2439 6392 0.038892 GCTCGTTTGAGACACGGGTA 60.039 55.000 0.00 0.00 45.57 3.69
2505 6458 0.681887 TCGCGAGACCCAGAACCATA 60.682 55.000 3.71 0.00 33.31 2.74
2580 6533 2.989840 CACTTCCTTCTCGTTGCTGTAG 59.010 50.000 0.00 0.00 0.00 2.74
2647 6600 3.155998 CACATTGCAGATCGTCGAAAAC 58.844 45.455 0.00 0.00 0.00 2.43
2736 6708 7.226720 TCACAAGAAGATGGACTAAAGTTGAAC 59.773 37.037 0.00 0.00 0.00 3.18
2762 6774 2.198827 TGTTCACCGAAATGATGCCT 57.801 45.000 0.00 0.00 0.00 4.75
2765 6777 7.420002 ACATATTGATGTTCACCGAAATGATG 58.580 34.615 0.00 0.00 44.18 3.07
2775 6800 6.128715 CCGAGATGCTACATATTGATGTTCAC 60.129 42.308 0.00 0.00 44.18 3.18
2805 6831 7.764443 TGCAATCAGTACATCTTTAGAGTAACC 59.236 37.037 0.00 0.00 0.00 2.85
2814 6840 4.083324 CCACGTTGCAATCAGTACATCTTT 60.083 41.667 0.59 0.00 0.00 2.52
3170 7240 8.508062 GTGGTACAAGTTTTGGTTTGAAATTTT 58.492 29.630 0.00 0.00 44.16 1.82
3205 7277 0.856641 CGAGAAGCCGACGAAACAAA 59.143 50.000 0.00 0.00 0.00 2.83
3409 12696 3.068560 CGGTAACCAAATTCCTGACGAA 58.931 45.455 0.00 0.00 34.14 3.85
3433 12724 1.448540 GCTGGTGACATGGAGACGG 60.449 63.158 0.00 0.00 41.51 4.79
3470 12761 1.072505 TTGGGTGACGCTTCCTTCC 59.927 57.895 0.31 0.00 0.00 3.46
3493 12791 6.868339 CCTACAAAAATCACCAAAACAGATCC 59.132 38.462 0.00 0.00 0.00 3.36
3518 12817 0.596083 CCATCGCCATCTCACGTCTC 60.596 60.000 0.00 0.00 0.00 3.36
3557 12868 3.872696 TCATCGTATCAAGTGCCATGTT 58.127 40.909 0.00 0.00 0.00 2.71
3558 12869 3.541996 TCATCGTATCAAGTGCCATGT 57.458 42.857 0.00 0.00 0.00 3.21
3819 13160 3.112580 CCGTTCGTCAGCAACAAATTTT 58.887 40.909 0.00 0.00 0.00 1.82
3824 13165 0.460459 TGTCCGTTCGTCAGCAACAA 60.460 50.000 0.00 0.00 0.00 2.83
3825 13166 0.460459 TTGTCCGTTCGTCAGCAACA 60.460 50.000 0.00 0.00 0.00 3.33
3846 13201 1.029408 TTCGATCCGGCCATTGGTTG 61.029 55.000 2.24 0.00 0.00 3.77
3855 13210 2.106683 CCTGGTGTTTCGATCCGGC 61.107 63.158 0.00 0.00 0.00 6.13
3856 13211 1.449601 CCCTGGTGTTTCGATCCGG 60.450 63.158 0.00 0.00 0.00 5.14
3857 13212 0.321298 AACCCTGGTGTTTCGATCCG 60.321 55.000 0.00 0.00 0.00 4.18
3858 13213 1.165270 CAACCCTGGTGTTTCGATCC 58.835 55.000 0.00 0.00 0.00 3.36
3859 13214 0.521735 GCAACCCTGGTGTTTCGATC 59.478 55.000 0.00 0.00 0.00 3.69
3860 13215 0.893727 GGCAACCCTGGTGTTTCGAT 60.894 55.000 0.00 0.00 0.00 3.59
3861 13216 1.527380 GGCAACCCTGGTGTTTCGA 60.527 57.895 0.00 0.00 0.00 3.71
3862 13217 2.903547 CGGCAACCCTGGTGTTTCG 61.904 63.158 0.00 0.61 0.00 3.46
3863 13218 2.561037 CCGGCAACCCTGGTGTTTC 61.561 63.158 0.00 0.00 0.00 2.78
3864 13219 2.366153 ATCCGGCAACCCTGGTGTTT 62.366 55.000 0.00 0.00 0.00 2.83
3865 13220 2.840753 ATCCGGCAACCCTGGTGTT 61.841 57.895 0.00 0.00 0.00 3.32
3866 13221 3.256960 ATCCGGCAACCCTGGTGT 61.257 61.111 0.00 0.00 0.00 4.16
3867 13222 2.751436 CATCCGGCAACCCTGGTG 60.751 66.667 0.00 0.00 0.00 4.17
3868 13223 2.366153 AAACATCCGGCAACCCTGGT 62.366 55.000 0.00 0.00 0.00 4.00
3869 13224 1.184970 AAAACATCCGGCAACCCTGG 61.185 55.000 0.00 0.00 0.00 4.45
3870 13225 0.243636 GAAAACATCCGGCAACCCTG 59.756 55.000 0.00 0.00 0.00 4.45
3871 13226 0.112412 AGAAAACATCCGGCAACCCT 59.888 50.000 0.00 0.00 0.00 4.34
3872 13227 0.966179 AAGAAAACATCCGGCAACCC 59.034 50.000 0.00 0.00 0.00 4.11
3873 13228 1.401018 CGAAGAAAACATCCGGCAACC 60.401 52.381 0.00 0.00 0.00 3.77
3874 13229 1.265905 ACGAAGAAAACATCCGGCAAC 59.734 47.619 0.00 0.00 0.00 4.17
3875 13230 1.265635 CACGAAGAAAACATCCGGCAA 59.734 47.619 0.00 0.00 0.00 4.52
3876 13231 0.871722 CACGAAGAAAACATCCGGCA 59.128 50.000 0.00 0.00 0.00 5.69
3877 13232 0.454452 GCACGAAGAAAACATCCGGC 60.454 55.000 0.00 0.00 0.00 6.13
3878 13233 1.128692 GAGCACGAAGAAAACATCCGG 59.871 52.381 0.00 0.00 0.00 5.14
3879 13234 1.128692 GGAGCACGAAGAAAACATCCG 59.871 52.381 0.00 0.00 0.00 4.18
3880 13235 2.902065 GGAGCACGAAGAAAACATCC 57.098 50.000 0.00 0.00 0.00 3.51
3911 13266 0.174845 CGGTTCTGGCGGTGAATAGA 59.825 55.000 0.00 0.00 0.00 1.98
3969 13373 4.570663 CGGGAGACGGCGATGGAC 62.571 72.222 16.62 0.00 39.42 4.02
3979 13383 1.298859 GCCATGTGTTGACGGGAGAC 61.299 60.000 0.00 0.00 0.00 3.36
4003 13423 4.400961 AGAAGGTCAGCCGGCTGC 62.401 66.667 44.77 36.99 43.31 5.25
4005 13425 3.394836 GGAGAAGGTCAGCCGGCT 61.395 66.667 27.08 27.08 40.50 5.52
4006 13426 4.821589 CGGAGAAGGTCAGCCGGC 62.822 72.222 21.89 21.89 40.08 6.13
4009 13429 4.821589 CGCCGGAGAAGGTCAGCC 62.822 72.222 5.05 0.00 0.00 4.85
4010 13430 3.708220 CTCGCCGGAGAAGGTCAGC 62.708 68.421 9.83 0.00 43.27 4.26
4011 13431 2.492090 CTCGCCGGAGAAGGTCAG 59.508 66.667 9.83 0.00 43.27 3.51
4012 13432 3.760035 GCTCGCCGGAGAAGGTCA 61.760 66.667 9.83 0.00 43.27 4.02
4051 13510 2.043227 GTTAGAGGCAGCCCTGAGTAT 58.957 52.381 8.22 0.00 43.12 2.12
4055 13514 0.978146 GGAGTTAGAGGCAGCCCTGA 60.978 60.000 8.22 0.00 43.12 3.86
4069 15779 4.077822 CAGATCAAGAGGCTTTTGGAGTT 58.922 43.478 16.72 1.41 0.00 3.01
4070 15780 3.560882 CCAGATCAAGAGGCTTTTGGAGT 60.561 47.826 16.72 4.76 0.00 3.85
4071 15781 3.015327 CCAGATCAAGAGGCTTTTGGAG 58.985 50.000 16.72 5.58 0.00 3.86
4102 15831 3.827008 AGATCATTTAGCTTCTGCGGA 57.173 42.857 0.00 0.00 45.42 5.54
4119 15848 7.736691 TGGGATCATCAGGAGATAGTTTTAGAT 59.263 37.037 0.00 0.00 31.88 1.98
4120 15849 7.075797 TGGGATCATCAGGAGATAGTTTTAGA 58.924 38.462 0.00 0.00 31.88 2.10
4132 17021 4.202556 TGTTGACTTTTGGGATCATCAGGA 60.203 41.667 0.00 0.00 0.00 3.86
4186 17090 0.729116 GTGTGATGGTCCTGCATTCG 59.271 55.000 0.00 0.00 0.00 3.34
4205 17109 2.690778 GGGTGCCTTTGCTGCTACG 61.691 63.158 0.00 0.00 38.71 3.51
4226 17130 4.268405 GCAACCAAACAAGCATATATGTGC 59.732 41.667 16.01 16.01 45.38 4.57
4269 17173 4.252073 AGGATCTTCGATATGATGCAAGC 58.748 43.478 14.04 0.00 34.21 4.01
4290 17194 1.258445 ACTAGGCCAACCTCACCGAG 61.258 60.000 5.01 0.00 46.34 4.63
4292 17196 0.673644 CAACTAGGCCAACCTCACCG 60.674 60.000 5.01 0.00 46.34 4.94
4293 17197 0.690762 TCAACTAGGCCAACCTCACC 59.309 55.000 5.01 0.00 46.34 4.02
4303 17207 7.617041 AATCTTTACATCTGTTCAACTAGGC 57.383 36.000 0.00 0.00 0.00 3.93


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

AutoCloner maintained by Alex Coulton.