Multiple sequence alignment - TraesCS2A01G172500

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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 TraesCS2A01G172500 chr2A 100.000 4409 0 0 1 4409 129096888 129101296 0.000000e+00 8142.0
1 TraesCS2A01G172500 chr2D 93.792 2996 142 26 2 2981 123802796 123805763 0.000000e+00 4462.0
2 TraesCS2A01G172500 chr2D 95.299 1404 41 9 3020 4409 123805764 123807156 0.000000e+00 2204.0
3 TraesCS2A01G172500 chr2B 92.976 3004 130 43 3 2981 176405768 176408715 0.000000e+00 4303.0
4 TraesCS2A01G172500 chr2B 89.829 1406 72 26 3020 4409 176408716 176410066 0.000000e+00 1738.0
5 TraesCS2A01G172500 chr3A 93.950 876 44 5 1503 2376 729020131 729020999 0.000000e+00 1315.0
6 TraesCS2A01G172500 chr3A 97.917 48 0 1 2981 3028 335474168 335474214 1.020000e-11 82.4
7 TraesCS2A01G172500 chr7B 92.040 402 20 4 1986 2376 504225080 504225480 4.980000e-154 555.0
8 TraesCS2A01G172500 chr7B 89.736 341 18 7 1497 1836 504224757 504225081 1.900000e-113 420.0
9 TraesCS2A01G172500 chr1B 92.040 402 20 4 1986 2376 101250659 101250259 4.980000e-154 555.0
10 TraesCS2A01G172500 chr1B 90.029 341 17 7 1497 1836 101250982 101250658 4.080000e-115 425.0
11 TraesCS2A01G172500 chr5B 100.000 45 0 0 2982 3026 635464514 635464470 2.830000e-12 84.2
12 TraesCS2A01G172500 chr1D 97.917 48 1 0 2982 3029 249030360 249030313 2.830000e-12 84.2
13 TraesCS2A01G172500 chr1D 95.349 43 2 0 1378 1420 106843111 106843153 7.910000e-08 69.4
14 TraesCS2A01G172500 chr1A 97.917 48 1 0 2982 3029 298603648 298603695 2.830000e-12 84.2
15 TraesCS2A01G172500 chr1A 100.000 44 0 0 2981 3024 464836364 464836321 1.020000e-11 82.4
16 TraesCS2A01G172500 chr5D 100.000 44 0 0 2981 3024 191259067 191259024 1.020000e-11 82.4
17 TraesCS2A01G172500 chr3D 97.917 48 0 1 2981 3028 254106914 254106868 1.020000e-11 82.4
18 TraesCS2A01G172500 chr3D 95.745 47 1 1 1375 1420 587100536 587100490 1.700000e-09 75.0
19 TraesCS2A01G172500 chr3B 97.917 48 0 1 2981 3028 305531570 305531524 1.020000e-11 82.4
20 TraesCS2A01G172500 chr3B 93.478 46 3 0 1375 1420 194074817 194074772 7.910000e-08 69.4
21 TraesCS2A01G172500 chr6B 96.000 50 1 1 2982 3031 409289964 409289916 3.660000e-11 80.5
22 TraesCS2A01G172500 chr6D 97.561 41 1 0 1380 1420 24231419 24231459 2.200000e-08 71.3
23 TraesCS2A01G172500 chr6D 97.561 41 1 0 1380 1420 97555493 97555453 2.200000e-08 71.3
24 TraesCS2A01G172500 chr7D 91.667 48 3 1 1374 1420 127000981 127000934 1.020000e-06 65.8
25 TraesCS2A01G172500 chr4A 90.000 50 4 1 1371 1420 236160809 236160761 3.680000e-06 63.9


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 TraesCS2A01G172500 chr2A 129096888 129101296 4408 False 8142.0 8142 100.0000 1 4409 1 chr2A.!!$F1 4408
1 TraesCS2A01G172500 chr2D 123802796 123807156 4360 False 3333.0 4462 94.5455 2 4409 2 chr2D.!!$F1 4407
2 TraesCS2A01G172500 chr2B 176405768 176410066 4298 False 3020.5 4303 91.4025 3 4409 2 chr2B.!!$F1 4406
3 TraesCS2A01G172500 chr3A 729020131 729020999 868 False 1315.0 1315 93.9500 1503 2376 1 chr3A.!!$F2 873
4 TraesCS2A01G172500 chr7B 504224757 504225480 723 False 487.5 555 90.8880 1497 2376 2 chr7B.!!$F1 879
5 TraesCS2A01G172500 chr1B 101250259 101250982 723 True 490.0 555 91.0345 1497 2376 2 chr1B.!!$R1 879

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
865 870 0.541863 CAAAGTGATAGGGGGTCGCT 59.458 55.000 0.0 0.0 38.02 4.93 F
1288 1295 0.179018 GCAACACACCTCAAGACCCT 60.179 55.000 0.0 0.0 0.00 4.34 F
1656 1674 1.631388 TCTCCGAAGCCCCATTTACAA 59.369 47.619 0.0 0.0 0.00 2.41 F
3129 3167 0.741915 GGCGGTTCCTCAACACAAAA 59.258 50.000 0.0 0.0 33.70 2.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2809 2847 1.204146 ATGTACTGCGGGGTCAGATT 58.796 50.000 0.00 0.0 37.51 2.40 R
3129 3167 0.037790 GCTTCTGCTCCTCGAGTTGT 60.038 55.000 12.31 0.0 36.03 3.32 R
3246 3284 0.102300 AAAAGCTTGACACGTTGGCC 59.898 50.000 0.00 0.0 0.00 5.36 R
4078 4132 4.806640 TTGAGGGCAGAATTTCCATTTC 57.193 40.909 0.00 0.0 0.00 2.17 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
29 30 1.794116 CTTTTGCAGGATTTGTTGGCG 59.206 47.619 0.00 0.00 0.00 5.69
88 89 5.954296 CTGATTGACAGTGACAGGAAAAT 57.046 39.130 0.00 0.00 41.30 1.82
118 119 5.336150 AGTTCATATGGACAGTGTCTGAG 57.664 43.478 22.18 8.86 35.18 3.35
132 133 2.438021 TGTCTGAGTAGGCCTTTGTTGT 59.562 45.455 12.58 0.00 0.00 3.32
195 196 2.826128 GGAATTCTGGGGTTGGAACTTC 59.174 50.000 5.23 0.00 0.00 3.01
196 197 3.496331 GAATTCTGGGGTTGGAACTTCA 58.504 45.455 0.00 0.00 0.00 3.02
201 202 1.460699 GGGTTGGAACTTCAGGCCT 59.539 57.895 0.00 0.00 0.00 5.19
232 233 7.560626 TCCTCCACTAAAAGTAGTCTAGGATTC 59.439 40.741 8.62 0.00 40.36 2.52
307 308 3.186613 GTGCTTAGGGAAGAAAACTGACG 59.813 47.826 0.00 0.00 34.25 4.35
317 318 6.319399 GGAAGAAAACTGACGTTTCTTGAAA 58.681 36.000 15.05 0.00 42.28 2.69
334 335 6.634805 TCTTGAAAGTAGGACTATTCAGCAG 58.365 40.000 0.00 0.00 31.80 4.24
568 571 3.055819 TCTCGGATGATGCTAATTAGGCC 60.056 47.826 14.28 0.00 0.00 5.19
587 590 4.042187 AGGCCAGATATGTCCCATTTCTAC 59.958 45.833 5.01 0.00 0.00 2.59
606 609 4.901250 TCTACATATGCTGGACATTCCTGA 59.099 41.667 1.58 0.00 40.38 3.86
682 685 4.037446 GGATGCCGCTTATTTGTTGGAATA 59.963 41.667 0.00 0.00 0.00 1.75
741 744 9.167311 ACTCCGATATTGCCAATTATCTATTTC 57.833 33.333 0.00 0.00 0.00 2.17
742 745 8.506168 TCCGATATTGCCAATTATCTATTTCC 57.494 34.615 0.00 0.00 0.00 3.13
776 780 6.683974 AATATATCTGTTTGTCTGGTGTGC 57.316 37.500 0.00 0.00 0.00 4.57
784 788 7.041721 TCTGTTTGTCTGGTGTGCTATAATAG 58.958 38.462 0.00 0.00 0.00 1.73
862 867 7.514721 TGATATAAACAAAGTGATAGGGGGTC 58.485 38.462 0.00 0.00 0.00 4.46
865 870 0.541863 CAAAGTGATAGGGGGTCGCT 59.458 55.000 0.00 0.00 38.02 4.93
877 882 2.546494 GGTCGCTGCTGCAACTGTT 61.546 57.895 16.29 0.00 39.64 3.16
878 883 1.082496 GTCGCTGCTGCAACTGTTC 60.082 57.895 16.29 0.00 39.64 3.18
982 988 3.067742 GCTTGGAGCTAAGTGATACCGTA 59.932 47.826 0.00 0.00 38.45 4.02
1000 1006 9.825972 GATACCGTAATATAACGCTAACACTTA 57.174 33.333 0.00 0.00 41.51 2.24
1130 1137 0.935898 CTTATCAGCTGGCTTCTGCG 59.064 55.000 15.13 0.00 40.82 5.18
1159 1166 3.445096 GGATTTCTTGTCAGGGAATGGTG 59.555 47.826 0.00 0.00 0.00 4.17
1160 1167 3.593442 TTTCTTGTCAGGGAATGGTGT 57.407 42.857 0.00 0.00 0.00 4.16
1170 1177 4.080582 TCAGGGAATGGTGTTCATACGAAT 60.081 41.667 0.00 0.00 34.44 3.34
1258 1265 1.458445 CATCTGCAACGAGTGACAGTG 59.542 52.381 0.00 0.00 34.72 3.66
1288 1295 0.179018 GCAACACACCTCAAGACCCT 60.179 55.000 0.00 0.00 0.00 4.34
1324 1331 7.822658 TGGTAATGCTTTATCTTTAACCACAC 58.177 34.615 4.45 0.00 0.00 3.82
1343 1350 4.623167 CACACTGTCACACTAGTAATCTGC 59.377 45.833 0.00 0.00 0.00 4.26
1346 1353 6.152831 ACACTGTCACACTAGTAATCTGCATA 59.847 38.462 0.00 0.00 0.00 3.14
1375 1382 5.582269 TGCAGTTTCAGCTCTTATGATGTAC 59.418 40.000 0.00 0.00 0.00 2.90
1376 1383 5.814705 GCAGTTTCAGCTCTTATGATGTACT 59.185 40.000 0.00 0.00 0.00 2.73
1378 1385 7.492669 GCAGTTTCAGCTCTTATGATGTACTAA 59.507 37.037 0.00 0.00 0.00 2.24
1379 1386 8.812329 CAGTTTCAGCTCTTATGATGTACTAAC 58.188 37.037 0.00 0.00 0.00 2.34
1380 1387 8.531982 AGTTTCAGCTCTTATGATGTACTAACA 58.468 33.333 0.00 0.00 40.69 2.41
1381 1388 8.812329 GTTTCAGCTCTTATGATGTACTAACAG 58.188 37.037 0.00 0.00 39.49 3.16
1382 1389 7.646548 TCAGCTCTTATGATGTACTAACAGT 57.353 36.000 0.00 0.00 39.49 3.55
1383 1390 7.484140 TCAGCTCTTATGATGTACTAACAGTG 58.516 38.462 0.00 0.00 39.49 3.66
1384 1391 7.122799 TCAGCTCTTATGATGTACTAACAGTGT 59.877 37.037 0.00 0.00 39.49 3.55
1385 1392 7.433719 CAGCTCTTATGATGTACTAACAGTGTC 59.566 40.741 0.00 0.00 39.49 3.67
1426 1433 3.055094 TGAGGCAGAGGGAGTAACAATTC 60.055 47.826 0.00 0.00 0.00 2.17
1427 1434 3.185455 AGGCAGAGGGAGTAACAATTCT 58.815 45.455 0.00 0.00 0.00 2.40
1428 1435 3.589288 AGGCAGAGGGAGTAACAATTCTT 59.411 43.478 0.00 0.00 0.00 2.52
1432 1439 5.390991 GCAGAGGGAGTAACAATTCTTTTCG 60.391 44.000 0.00 0.00 0.00 3.46
1437 1444 5.849604 GGGAGTAACAATTCTTTTCGTTTCG 59.150 40.000 0.00 0.00 0.00 3.46
1442 1449 5.843255 ACAATTCTTTTCGTTTCGTTTCG 57.157 34.783 0.00 0.00 0.00 3.46
1452 1459 3.613737 TCGTTTCGTTTCGTTTCTGAGTT 59.386 39.130 0.00 0.00 0.00 3.01
1495 1502 5.564063 GCCTGTATTTTAATTATCGGCCACC 60.564 44.000 2.24 0.00 0.00 4.61
1532 1549 6.127619 GCTTCTTACCAATGCCTAAACTCATT 60.128 38.462 0.00 0.00 33.56 2.57
1538 1555 6.340522 ACCAATGCCTAAACTCATTATTTGC 58.659 36.000 0.00 0.00 32.22 3.68
1539 1556 6.070881 ACCAATGCCTAAACTCATTATTTGCA 60.071 34.615 0.00 0.00 32.22 4.08
1622 1640 5.053811 GCTTTATTAGTGGCTCTTCTCTCC 58.946 45.833 0.00 0.00 0.00 3.71
1656 1674 1.631388 TCTCCGAAGCCCCATTTACAA 59.369 47.619 0.00 0.00 0.00 2.41
1671 1689 7.205297 CCCATTTACAATGAGGTGAATTGATC 58.795 38.462 3.32 0.00 38.21 2.92
1869 1887 9.381033 CATGGGAATTGTTCTCTATCTCATATC 57.619 37.037 0.00 0.00 0.00 1.63
2212 2242 4.292977 AGCAACAGAACACACTAAAAGC 57.707 40.909 0.00 0.00 0.00 3.51
2224 2254 5.818857 ACACACTAAAAGCGTCCTCTTAAAA 59.181 36.000 0.00 0.00 0.00 1.52
2237 2267 7.763071 GCGTCCTCTTAAAAGGATAAAGAAGTA 59.237 37.037 0.00 0.00 46.90 2.24
2240 2270 9.939802 TCCTCTTAAAAGGATAAAGAAGTACAC 57.060 33.333 0.00 0.00 40.60 2.90
2255 2285 7.484035 AGAAGTACACAAACAGATCTTTCAC 57.516 36.000 0.00 0.00 0.00 3.18
2615 2653 2.159085 AGGAGGCAGATACGTGCTAAAC 60.159 50.000 0.00 0.00 43.45 2.01
2780 2818 9.712305 GATTTCAGCTACAGATTTATTAGGCTA 57.288 33.333 0.00 0.00 0.00 3.93
2805 2843 8.388656 ACCTTGGTAATATTCAGAGGACTAAA 57.611 34.615 11.75 0.00 0.00 1.85
2806 2844 9.004231 ACCTTGGTAATATTCAGAGGACTAAAT 57.996 33.333 11.75 0.00 0.00 1.40
2807 2845 9.495572 CCTTGGTAATATTCAGAGGACTAAATC 57.504 37.037 0.00 0.00 0.00 2.17
2819 2857 5.841783 AGAGGACTAAATCTAATCTGACCCC 59.158 44.000 0.00 0.00 0.00 4.95
2820 2858 4.589374 AGGACTAAATCTAATCTGACCCCG 59.411 45.833 0.00 0.00 0.00 5.73
2821 2859 4.308265 GACTAAATCTAATCTGACCCCGC 58.692 47.826 0.00 0.00 0.00 6.13
2879 2917 2.903135 GGCAGAGGCATATTCCTAGTCT 59.097 50.000 0.00 0.00 43.71 3.24
2880 2918 3.326297 GGCAGAGGCATATTCCTAGTCTT 59.674 47.826 0.00 0.00 43.71 3.01
2881 2919 4.528596 GGCAGAGGCATATTCCTAGTCTTA 59.471 45.833 0.00 0.00 43.71 2.10
2885 2923 7.039644 GCAGAGGCATATTCCTAGTCTTAAGTA 60.040 40.741 1.63 0.00 40.72 2.24
2901 2939 7.663905 AGTCTTAAGTACATACCATGTTGCAAA 59.336 33.333 0.00 0.00 41.63 3.68
2956 2994 3.450904 TGAAGGCTTGTACCCATCTACT 58.549 45.455 3.46 0.00 0.00 2.57
2992 3030 9.961265 AAGTTTTACCTAGCATTGAACTAAAAC 57.039 29.630 0.00 0.00 34.79 2.43
2993 3031 8.573885 AGTTTTACCTAGCATTGAACTAAAACC 58.426 33.333 0.00 0.00 34.99 3.27
2994 3032 8.354426 GTTTTACCTAGCATTGAACTAAAACCA 58.646 33.333 0.00 0.00 31.14 3.67
2995 3033 5.959618 ACCTAGCATTGAACTAAAACCAC 57.040 39.130 0.00 0.00 0.00 4.16
2996 3034 4.454504 ACCTAGCATTGAACTAAAACCACG 59.545 41.667 0.00 0.00 0.00 4.94
2997 3035 4.693566 CCTAGCATTGAACTAAAACCACGA 59.306 41.667 0.00 0.00 0.00 4.35
2998 3036 4.483476 AGCATTGAACTAAAACCACGAC 57.517 40.909 0.00 0.00 0.00 4.34
2999 3037 3.880490 AGCATTGAACTAAAACCACGACA 59.120 39.130 0.00 0.00 0.00 4.35
3000 3038 4.336993 AGCATTGAACTAAAACCACGACAA 59.663 37.500 0.00 0.00 0.00 3.18
3001 3039 4.675114 GCATTGAACTAAAACCACGACAAG 59.325 41.667 0.00 0.00 0.00 3.16
3002 3040 5.504994 GCATTGAACTAAAACCACGACAAGA 60.505 40.000 0.00 0.00 0.00 3.02
3003 3041 6.491394 CATTGAACTAAAACCACGACAAGAA 58.509 36.000 0.00 0.00 0.00 2.52
3004 3042 6.687081 TTGAACTAAAACCACGACAAGAAT 57.313 33.333 0.00 0.00 0.00 2.40
3005 3043 6.687081 TGAACTAAAACCACGACAAGAATT 57.313 33.333 0.00 0.00 0.00 2.17
3006 3044 7.789273 TGAACTAAAACCACGACAAGAATTA 57.211 32.000 0.00 0.00 0.00 1.40
3007 3045 8.385898 TGAACTAAAACCACGACAAGAATTAT 57.614 30.769 0.00 0.00 0.00 1.28
3008 3046 8.286800 TGAACTAAAACCACGACAAGAATTATG 58.713 33.333 0.00 0.00 0.00 1.90
3009 3047 7.141100 ACTAAAACCACGACAAGAATTATGG 57.859 36.000 0.00 0.00 0.00 2.74
3010 3048 6.938030 ACTAAAACCACGACAAGAATTATGGA 59.062 34.615 0.00 0.00 0.00 3.41
3011 3049 6.642707 AAAACCACGACAAGAATTATGGAA 57.357 33.333 0.00 0.00 0.00 3.53
3012 3050 5.622770 AACCACGACAAGAATTATGGAAC 57.377 39.130 0.00 0.00 0.00 3.62
3013 3051 3.682858 ACCACGACAAGAATTATGGAACG 59.317 43.478 0.00 0.00 0.00 3.95
3014 3052 3.063452 CCACGACAAGAATTATGGAACGG 59.937 47.826 0.00 0.00 0.00 4.44
3015 3053 3.930229 CACGACAAGAATTATGGAACGGA 59.070 43.478 0.00 0.00 0.00 4.69
3016 3054 4.032900 CACGACAAGAATTATGGAACGGAG 59.967 45.833 0.00 0.00 0.00 4.63
3017 3055 3.555956 CGACAAGAATTATGGAACGGAGG 59.444 47.826 0.00 0.00 0.00 4.30
3018 3056 3.877508 GACAAGAATTATGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
3019 3057 3.521937 ACAAGAATTATGGAACGGAGGGA 59.478 43.478 0.00 0.00 0.00 4.20
3020 3058 4.130118 CAAGAATTATGGAACGGAGGGAG 58.870 47.826 0.00 0.00 0.00 4.30
3021 3059 3.385115 AGAATTATGGAACGGAGGGAGT 58.615 45.455 0.00 0.00 0.00 3.85
3022 3060 4.553678 AGAATTATGGAACGGAGGGAGTA 58.446 43.478 0.00 0.00 0.00 2.59
3023 3061 4.344390 AGAATTATGGAACGGAGGGAGTAC 59.656 45.833 0.00 0.00 0.00 2.73
3024 3062 2.077687 TATGGAACGGAGGGAGTACC 57.922 55.000 0.00 0.00 40.67 3.34
3044 3082 3.264964 ACCTTTTCTAACATCGCCCCTTA 59.735 43.478 0.00 0.00 0.00 2.69
3048 3086 3.469008 TCTAACATCGCCCCTTACATG 57.531 47.619 0.00 0.00 0.00 3.21
3129 3167 0.741915 GGCGGTTCCTCAACACAAAA 59.258 50.000 0.00 0.00 33.70 2.44
3212 3250 3.055094 GGCAAGAATACACTCCTTCAGGA 60.055 47.826 0.00 0.00 43.08 3.86
3246 3284 2.587194 CCTTCGGCATCAGCTCCG 60.587 66.667 5.25 5.25 46.52 4.63
3247 3285 2.587194 CTTCGGCATCAGCTCCGG 60.587 66.667 11.27 0.00 45.31 5.14
3253 3291 3.197790 CATCAGCTCCGGCCAACG 61.198 66.667 2.24 0.00 43.80 4.10
3272 3310 4.370364 ACGTGTCAAGCTTTTCAACAAT 57.630 36.364 0.00 0.00 0.00 2.71
3274 3312 4.142491 ACGTGTCAAGCTTTTCAACAATCA 60.142 37.500 0.00 0.00 0.00 2.57
3330 3368 2.112297 GTTGGCTTCCGTCCCACA 59.888 61.111 0.00 0.00 0.00 4.17
3370 3408 3.294493 GCAACGGGAAGCTGGCAA 61.294 61.111 0.00 0.00 0.00 4.52
3378 3416 1.959226 GAAGCTGGCAACGAACGGA 60.959 57.895 0.00 0.00 42.51 4.69
3390 3428 3.039202 GAACGGAATGCACCAGCGG 62.039 63.158 0.00 0.00 46.23 5.52
3471 3509 3.627395 TGGCTTATGAAGATGTTCCGT 57.373 42.857 0.00 0.00 0.00 4.69
3517 3556 5.491982 GACCAAGACATTGTTATGAGTCCT 58.508 41.667 0.00 0.00 35.65 3.85
3587 3626 6.058553 TGTGGAGACTGAAATCTTCATCAT 57.941 37.500 0.00 0.00 36.58 2.45
3873 3925 3.565307 TGGGCTCTGAAACATGAACTTT 58.435 40.909 0.00 0.00 0.00 2.66
3879 3931 6.035843 GCTCTGAAACATGAACTTTCAAACA 58.964 36.000 0.00 0.00 41.13 2.83
3898 3952 7.555087 TCAAACAAACCTGAAAGTGATCAATT 58.445 30.769 1.80 1.80 0.00 2.32
3899 3953 8.690884 TCAAACAAACCTGAAAGTGATCAATTA 58.309 29.630 9.10 0.00 0.00 1.40
4078 4132 6.639632 ATTGCTTGCATATTAGTTACTGGG 57.360 37.500 0.00 0.00 0.00 4.45
4187 4241 5.241662 CAGAACTCAGGTTTAAAGGAGAGG 58.758 45.833 14.88 0.00 35.58 3.69
4402 4456 1.517832 CAGAACTAGGTGAGGGCCG 59.482 63.158 0.00 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.460255 CCTGCAAAAGGGGAGTCCA 59.540 57.895 12.30 0.00 43.15 4.02
88 89 6.551227 ACACTGTCCATATGAACTAGCATCTA 59.449 38.462 3.65 0.00 0.00 1.98
118 119 4.584327 ATCAAACACAACAAAGGCCTAC 57.416 40.909 5.16 0.00 0.00 3.18
195 196 1.053264 AGTGGAGGATGCTAGGCCTG 61.053 60.000 17.99 6.68 33.84 4.85
196 197 0.563173 TAGTGGAGGATGCTAGGCCT 59.437 55.000 11.78 11.78 37.18 5.19
201 202 6.195700 AGACTACTTTTAGTGGAGGATGCTA 58.804 40.000 0.00 0.00 38.77 3.49
232 233 0.038892 GCATGCAGAACACCAACAGG 60.039 55.000 14.21 0.00 0.00 4.00
307 308 7.387948 TGCTGAATAGTCCTACTTTCAAGAAAC 59.612 37.037 0.00 0.00 30.69 2.78
317 318 6.609212 TCAGATTTCTGCTGAATAGTCCTACT 59.391 38.462 6.88 0.00 43.46 2.57
334 335 4.986622 CCATTCGGGTTCTTTCAGATTTC 58.013 43.478 0.00 0.00 0.00 2.17
360 361 1.798813 CAGTCAAGGAAGGCGTGTTAC 59.201 52.381 0.00 0.00 0.00 2.50
416 417 4.746535 TCCAACATTAGAATAGACGGCA 57.253 40.909 0.00 0.00 0.00 5.69
549 552 3.005554 CTGGCCTAATTAGCATCATCCG 58.994 50.000 3.32 0.00 0.00 4.18
587 590 4.321008 GCAATCAGGAATGTCCAGCATATG 60.321 45.833 0.00 0.00 39.61 1.78
606 609 0.613012 GCCTGAACCAAGGGAGCAAT 60.613 55.000 0.00 0.00 37.84 3.56
753 757 6.418101 AGCACACCAGACAAACAGATATATT 58.582 36.000 0.00 0.00 0.00 1.28
765 769 6.731292 ATCACTATTATAGCACACCAGACA 57.269 37.500 0.00 0.00 0.00 3.41
784 788 4.082571 ACTTGCAGTTCATTAGGCAATCAC 60.083 41.667 0.00 0.00 44.32 3.06
862 867 0.029834 AAAGAACAGTTGCAGCAGCG 59.970 50.000 2.55 1.85 46.23 5.18
865 870 3.020274 TGGTAAAAGAACAGTTGCAGCA 58.980 40.909 2.55 0.00 0.00 4.41
1000 1006 6.066690 CAGGATGATCCTCCATTTTACACAT 58.933 40.000 11.91 0.00 45.66 3.21
1086 1093 3.005578 TGTTATTTGTGGCGTAAAACCCC 59.994 43.478 0.00 0.00 0.00 4.95
1087 1094 4.240175 TGTTATTTGTGGCGTAAAACCC 57.760 40.909 0.00 0.00 0.00 4.11
1088 1095 5.749588 AGTTTGTTATTTGTGGCGTAAAACC 59.250 36.000 0.00 0.00 0.00 3.27
1089 1096 6.815672 AGTTTGTTATTTGTGGCGTAAAAC 57.184 33.333 0.00 0.00 0.00 2.43
1130 1137 1.324736 CTGACAAGAAATCCTACGCGC 59.675 52.381 5.73 0.00 0.00 6.86
1170 1177 8.131100 CGGTCGTAGTTCTTATGGACTAATTTA 58.869 37.037 0.00 0.00 0.00 1.40
1179 1186 2.026641 TCCCGGTCGTAGTTCTTATGG 58.973 52.381 0.00 0.00 0.00 2.74
1258 1265 3.412386 AGGTGTGTTGCTCATTTAGACC 58.588 45.455 0.00 0.00 0.00 3.85
1288 1295 7.994911 AGATAAAGCATTACCAGATTGTGATGA 59.005 33.333 0.00 0.00 35.00 2.92
1324 1331 7.656412 AGATATGCAGATTACTAGTGTGACAG 58.344 38.462 5.39 0.00 0.00 3.51
1343 1350 4.695396 AGAGCTGAAACTGCAGAGATATG 58.305 43.478 23.35 6.85 38.14 1.78
1346 1353 3.699411 AAGAGCTGAAACTGCAGAGAT 57.301 42.857 23.35 5.51 38.14 2.75
1392 1399 4.752101 CCCTCTGCCTCAAAATATAAGACG 59.248 45.833 0.00 0.00 0.00 4.18
1426 1433 5.016985 TCAGAAACGAAACGAAACGAAAAG 58.983 37.500 0.00 0.00 0.00 2.27
1427 1434 4.955617 TCAGAAACGAAACGAAACGAAAA 58.044 34.783 0.00 0.00 0.00 2.29
1428 1435 4.091800 ACTCAGAAACGAAACGAAACGAAA 59.908 37.500 0.00 0.00 0.00 3.46
1432 1439 5.900242 CCTAAACTCAGAAACGAAACGAAAC 59.100 40.000 0.00 0.00 0.00 2.78
1437 1444 6.073440 TGCATACCTAAACTCAGAAACGAAAC 60.073 38.462 0.00 0.00 0.00 2.78
1442 1449 8.893727 ACATAATGCATACCTAAACTCAGAAAC 58.106 33.333 0.00 0.00 0.00 2.78
1452 1459 4.821260 CAGGCACACATAATGCATACCTAA 59.179 41.667 0.00 0.00 45.27 2.69
1495 1502 7.119846 GCATTGGTAAGAAGCATAGTAATAGGG 59.880 40.741 0.00 0.00 32.06 3.53
1638 1656 2.025793 TCATTGTAAATGGGGCTTCGGA 60.026 45.455 0.42 0.00 0.00 4.55
1656 1674 8.766476 AGATATAATCGGATCAATTCACCTCAT 58.234 33.333 0.00 0.00 0.00 2.90
1671 1689 9.639601 TTACTGTTAGCATGAAGATATAATCGG 57.360 33.333 0.00 0.00 0.00 4.18
1869 1887 1.239968 GCTGGTCAACTGAAGGCAGG 61.240 60.000 0.00 0.00 46.60 4.85
2224 2254 8.598041 AGATCTGTTTGTGTACTTCTTTATCCT 58.402 33.333 0.00 0.00 0.00 3.24
2255 2285 5.356882 TCAAGTCCTTAATGCGAAAACAG 57.643 39.130 0.00 0.00 0.00 3.16
2407 2444 6.332635 TGATAAATATGACAAGGGAGGGACAT 59.667 38.462 0.00 0.00 0.00 3.06
2408 2445 5.669904 TGATAAATATGACAAGGGAGGGACA 59.330 40.000 0.00 0.00 0.00 4.02
2409 2446 6.187727 TGATAAATATGACAAGGGAGGGAC 57.812 41.667 0.00 0.00 0.00 4.46
2410 2447 6.840090 TTGATAAATATGACAAGGGAGGGA 57.160 37.500 0.00 0.00 0.00 4.20
2615 2653 1.753073 CAGCTTATTTTGGGCCTCCAG 59.247 52.381 4.53 0.00 45.04 3.86
2780 2818 7.989947 TTAGTCCTCTGAATATTACCAAGGT 57.010 36.000 0.00 0.00 0.00 3.50
2805 2843 1.794714 ACTGCGGGGTCAGATTAGAT 58.205 50.000 0.00 0.00 37.51 1.98
2806 2844 2.029623 GTACTGCGGGGTCAGATTAGA 58.970 52.381 0.00 0.00 37.51 2.10
2807 2845 1.754803 TGTACTGCGGGGTCAGATTAG 59.245 52.381 0.00 0.00 37.51 1.73
2808 2846 1.855295 TGTACTGCGGGGTCAGATTA 58.145 50.000 0.00 0.00 37.51 1.75
2809 2847 1.204146 ATGTACTGCGGGGTCAGATT 58.796 50.000 0.00 0.00 37.51 2.40
2810 2848 1.204146 AATGTACTGCGGGGTCAGAT 58.796 50.000 0.00 0.00 37.51 2.90
2879 2917 7.543868 GCAATTTGCAACATGGTATGTACTTAA 59.456 33.333 16.35 0.00 44.26 1.85
2880 2918 7.032580 GCAATTTGCAACATGGTATGTACTTA 58.967 34.615 16.35 0.00 44.26 2.24
2881 2919 5.868801 GCAATTTGCAACATGGTATGTACTT 59.131 36.000 16.35 0.00 44.26 2.24
2901 2939 5.057819 TGCTGAACAAATGAATGTTGCAAT 58.942 33.333 0.59 0.00 43.31 3.56
2981 3019 6.687081 ATTCTTGTCGTGGTTTTAGTTCAA 57.313 33.333 0.00 0.00 0.00 2.69
2982 3020 6.687081 AATTCTTGTCGTGGTTTTAGTTCA 57.313 33.333 0.00 0.00 0.00 3.18
2983 3021 7.749126 CCATAATTCTTGTCGTGGTTTTAGTTC 59.251 37.037 0.00 0.00 0.00 3.01
2985 3023 6.938030 TCCATAATTCTTGTCGTGGTTTTAGT 59.062 34.615 0.00 0.00 0.00 2.24
2988 3026 6.443792 GTTCCATAATTCTTGTCGTGGTTTT 58.556 36.000 0.00 0.00 0.00 2.43
2989 3027 5.334569 CGTTCCATAATTCTTGTCGTGGTTT 60.335 40.000 0.00 0.00 0.00 3.27
2990 3028 4.153475 CGTTCCATAATTCTTGTCGTGGTT 59.847 41.667 0.00 0.00 0.00 3.67
2991 3029 3.682858 CGTTCCATAATTCTTGTCGTGGT 59.317 43.478 0.00 0.00 0.00 4.16
2992 3030 3.063452 CCGTTCCATAATTCTTGTCGTGG 59.937 47.826 0.00 0.00 0.00 4.94
2993 3031 3.930229 TCCGTTCCATAATTCTTGTCGTG 59.070 43.478 0.00 0.00 0.00 4.35
2994 3032 4.181578 CTCCGTTCCATAATTCTTGTCGT 58.818 43.478 0.00 0.00 0.00 4.34
2995 3033 3.555956 CCTCCGTTCCATAATTCTTGTCG 59.444 47.826 0.00 0.00 0.00 4.35
2996 3034 3.877508 CCCTCCGTTCCATAATTCTTGTC 59.122 47.826 0.00 0.00 0.00 3.18
2997 3035 3.521937 TCCCTCCGTTCCATAATTCTTGT 59.478 43.478 0.00 0.00 0.00 3.16
2998 3036 4.130118 CTCCCTCCGTTCCATAATTCTTG 58.870 47.826 0.00 0.00 0.00 3.02
2999 3037 3.780850 ACTCCCTCCGTTCCATAATTCTT 59.219 43.478 0.00 0.00 0.00 2.52
3000 3038 3.385115 ACTCCCTCCGTTCCATAATTCT 58.615 45.455 0.00 0.00 0.00 2.40
3001 3039 3.840124 ACTCCCTCCGTTCCATAATTC 57.160 47.619 0.00 0.00 0.00 2.17
3002 3040 3.390311 GGTACTCCCTCCGTTCCATAATT 59.610 47.826 0.00 0.00 0.00 1.40
3003 3041 2.970640 GGTACTCCCTCCGTTCCATAAT 59.029 50.000 0.00 0.00 0.00 1.28
3004 3042 2.023695 AGGTACTCCCTCCGTTCCATAA 60.024 50.000 0.00 0.00 40.71 1.90
3005 3043 1.572415 AGGTACTCCCTCCGTTCCATA 59.428 52.381 0.00 0.00 40.71 2.74
3006 3044 0.338814 AGGTACTCCCTCCGTTCCAT 59.661 55.000 0.00 0.00 40.71 3.41
3007 3045 0.115745 AAGGTACTCCCTCCGTTCCA 59.884 55.000 0.00 0.00 45.47 3.53
3008 3046 1.273759 AAAGGTACTCCCTCCGTTCC 58.726 55.000 0.00 0.00 45.47 3.62
3009 3047 2.566279 AGAAAAGGTACTCCCTCCGTTC 59.434 50.000 0.00 0.00 45.47 3.95
3010 3048 2.617658 AGAAAAGGTACTCCCTCCGTT 58.382 47.619 0.00 0.00 45.47 4.44
3011 3049 2.322339 AGAAAAGGTACTCCCTCCGT 57.678 50.000 0.00 0.00 45.47 4.69
3012 3050 3.512724 TGTTAGAAAAGGTACTCCCTCCG 59.487 47.826 0.00 0.00 45.47 4.63
3013 3051 5.672503 GATGTTAGAAAAGGTACTCCCTCC 58.327 45.833 0.00 0.00 45.47 4.30
3014 3052 5.349809 CGATGTTAGAAAAGGTACTCCCTC 58.650 45.833 0.00 0.00 45.47 4.30
3016 3054 3.869832 GCGATGTTAGAAAAGGTACTCCC 59.130 47.826 0.00 0.00 38.49 4.30
3017 3055 3.869832 GGCGATGTTAGAAAAGGTACTCC 59.130 47.826 0.00 0.00 38.49 3.85
3018 3056 3.869832 GGGCGATGTTAGAAAAGGTACTC 59.130 47.826 0.00 0.00 38.49 2.59
3020 3058 2.941064 GGGGCGATGTTAGAAAAGGTAC 59.059 50.000 0.00 0.00 0.00 3.34
3021 3059 2.841881 AGGGGCGATGTTAGAAAAGGTA 59.158 45.455 0.00 0.00 0.00 3.08
3022 3060 1.633945 AGGGGCGATGTTAGAAAAGGT 59.366 47.619 0.00 0.00 0.00 3.50
3023 3061 2.420058 AGGGGCGATGTTAGAAAAGG 57.580 50.000 0.00 0.00 0.00 3.11
3024 3062 4.258543 TGTAAGGGGCGATGTTAGAAAAG 58.741 43.478 0.00 0.00 0.00 2.27
3025 3063 4.289238 TGTAAGGGGCGATGTTAGAAAA 57.711 40.909 0.00 0.00 0.00 2.29
3044 3082 2.092267 TCATGAAGGTATGGCTGCATGT 60.092 45.455 0.50 0.00 35.75 3.21
3048 3086 3.484407 AGATTCATGAAGGTATGGCTGC 58.516 45.455 14.54 0.00 0.00 5.25
3129 3167 0.037790 GCTTCTGCTCCTCGAGTTGT 60.038 55.000 12.31 0.00 36.03 3.32
3246 3284 0.102300 AAAAGCTTGACACGTTGGCC 59.898 50.000 0.00 0.00 0.00 5.36
3247 3285 1.202245 TGAAAAGCTTGACACGTTGGC 60.202 47.619 0.00 0.00 0.00 4.52
3253 3291 4.207841 GCTGATTGTTGAAAAGCTTGACAC 59.792 41.667 0.00 0.00 0.00 3.67
3272 3310 1.476291 CCTGATTAGCCAGCATGCTGA 60.476 52.381 42.21 26.34 46.30 4.26
3274 3312 0.841961 TCCTGATTAGCCAGCATGCT 59.158 50.000 16.30 16.30 45.38 3.79
3369 3407 1.852067 GCTGGTGCATTCCGTTCGTT 61.852 55.000 0.00 0.00 39.41 3.85
3370 3408 2.325082 GCTGGTGCATTCCGTTCGT 61.325 57.895 0.00 0.00 39.41 3.85
3378 3416 3.064324 GAAGCCCGCTGGTGCATT 61.064 61.111 0.00 0.00 39.64 3.56
3390 3428 2.620585 GCTTTACCTCATCATGGAAGCC 59.379 50.000 0.00 0.00 31.92 4.35
3471 3509 7.312154 GTCCAACTGATATTGCAACACATTTA 58.688 34.615 0.00 0.00 0.00 1.40
3517 3556 8.465999 TGCTTTCAACTAGATGAAACTCAAAAA 58.534 29.630 20.59 2.53 42.68 1.94
3556 3595 0.817654 TCAGTCTCCACATAGTGCCG 59.182 55.000 0.00 0.00 31.34 5.69
3623 3663 2.224892 CCGATCTCTGGGATAGTCAGGA 60.225 54.545 0.00 0.00 34.33 3.86
3873 3925 6.522625 TTGATCACTTTCAGGTTTGTTTGA 57.477 33.333 0.00 0.00 0.00 2.69
3922 3976 7.365497 TCTTATTGCTCCTCATTGACTCATA 57.635 36.000 0.00 0.00 0.00 2.15
4078 4132 4.806640 TTGAGGGCAGAATTTCCATTTC 57.193 40.909 0.00 0.00 0.00 2.17
4187 4241 6.747659 AAATTGATGTTGTGTCGCTAAAAC 57.252 33.333 0.00 0.00 0.00 2.43


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

AutoCloner maintained by Alex Coulton.