Multiple sequence alignment - TraesCS6B01G238800

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 TraesCS6B01G238800 chr6B 100.000 2701 0 0 1 2701 415865383 415862683 0.000000e+00 4988.0
1 TraesCS6B01G238800 chr6B 97.024 504 15 0 1225 1728 415789548 415789045 0.000000e+00 848.0
2 TraesCS6B01G238800 chr6B 95.312 128 6 0 1024 1151 415789903 415789776 1.270000e-48 204.0
3 TraesCS6B01G238800 chr6B 86.538 52 6 1 2112 2163 300881667 300881717 3.760000e-04 56.5
4 TraesCS6B01G238800 chr6B 86.538 52 6 1 2112 2163 420747678 420747728 3.760000e-04 56.5
5 TraesCS6B01G238800 chr6D 92.290 1297 69 18 481 1769 267515924 267514651 0.000000e+00 1812.0
6 TraesCS6B01G238800 chr6D 96.477 511 18 0 1218 1728 267237317 267236807 0.000000e+00 845.0
7 TraesCS6B01G238800 chr6D 90.083 363 29 6 2153 2510 267514160 267513800 5.270000e-127 464.0
8 TraesCS6B01G238800 chr6D 82.241 473 32 24 9 472 267516403 267515974 7.110000e-96 361.0
9 TraesCS6B01G238800 chr6D 86.111 216 19 9 1878 2084 267514412 267514199 3.500000e-54 222.0
10 TraesCS6B01G238800 chr6D 95.312 128 6 0 1024 1151 267237706 267237579 1.270000e-48 204.0
11 TraesCS6B01G238800 chr6A 89.930 1430 74 28 481 1855 381026894 381025480 0.000000e+00 1779.0
12 TraesCS6B01G238800 chr6A 95.898 512 20 1 1218 1728 380361718 380361207 0.000000e+00 828.0
13 TraesCS6B01G238800 chr6A 82.014 834 102 24 1878 2697 381025491 381024692 0.000000e+00 665.0
14 TraesCS6B01G238800 chr6A 85.934 391 35 10 83 472 381027318 381026947 1.510000e-107 399.0
15 TraesCS6B01G238800 chr5D 86.251 1091 93 32 766 1817 531972187 531971115 0.000000e+00 1131.0
16 TraesCS6B01G238800 chr5D 85.263 475 50 11 1220 1677 531901308 531900837 3.150000e-129 472.0
17 TraesCS6B01G238800 chr5D 94.928 138 6 1 1022 1159 531902141 531902005 5.860000e-52 215.0
18 TraesCS6B01G238800 chr5D 92.473 93 2 2 640 728 531972275 531972184 7.850000e-26 128.0
19 TraesCS6B01G238800 chr4A 85.950 1089 92 33 764 1818 640232144 640233205 0.000000e+00 1107.0
20 TraesCS6B01G238800 chr4A 89.247 93 5 3 640 728 640232058 640232149 7.910000e-21 111.0
21 TraesCS6B01G238800 chr4A 93.617 47 2 1 333 378 640218868 640218914 4.830000e-08 69.4
22 TraesCS6B01G238800 chr5B 85.612 973 83 27 766 1700 671188619 671187666 0.000000e+00 968.0
23 TraesCS6B01G238800 chr5B 85.714 350 33 12 818 1161 671138248 671137910 1.190000e-93 353.0
24 TraesCS6B01G238800 chr3A 84.615 91 11 3 2094 2183 686572207 686572295 1.330000e-13 87.9
25 TraesCS6B01G238800 chr3D 86.538 52 6 1 2112 2163 101562175 101562225 3.760000e-04 56.5
26 TraesCS6B01G238800 chr3B 86.792 53 4 3 2112 2163 526000442 526000492 3.760000e-04 56.5
27 TraesCS6B01G238800 chr3B 86.538 52 6 1 2112 2163 667859423 667859373 3.760000e-04 56.5
28 TraesCS6B01G238800 chr2B 86.538 52 6 1 2112 2163 411496101 411496051 3.760000e-04 56.5
29 TraesCS6B01G238800 chr1D 86.538 52 6 1 2112 2163 490356605 490356555 3.760000e-04 56.5


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 TraesCS6B01G238800 chr6B 415862683 415865383 2700 True 4988.000000 4988 100.000000 1 2701 1 chr6B.!!$R1 2700
1 TraesCS6B01G238800 chr6B 415789045 415789903 858 True 526.000000 848 96.168000 1024 1728 2 chr6B.!!$R2 704
2 TraesCS6B01G238800 chr6D 267513800 267516403 2603 True 714.750000 1812 87.681250 9 2510 4 chr6D.!!$R2 2501
3 TraesCS6B01G238800 chr6D 267236807 267237706 899 True 524.500000 845 95.894500 1024 1728 2 chr6D.!!$R1 704
4 TraesCS6B01G238800 chr6A 381024692 381027318 2626 True 947.666667 1779 85.959333 83 2697 3 chr6A.!!$R2 2614
5 TraesCS6B01G238800 chr6A 380361207 380361718 511 True 828.000000 828 95.898000 1218 1728 1 chr6A.!!$R1 510
6 TraesCS6B01G238800 chr5D 531971115 531972275 1160 True 629.500000 1131 89.362000 640 1817 2 chr5D.!!$R2 1177
7 TraesCS6B01G238800 chr5D 531900837 531902141 1304 True 343.500000 472 90.095500 1022 1677 2 chr5D.!!$R1 655
8 TraesCS6B01G238800 chr4A 640232058 640233205 1147 False 609.000000 1107 87.598500 640 1818 2 chr4A.!!$F2 1178
9 TraesCS6B01G238800 chr5B 671187666 671188619 953 True 968.000000 968 85.612000 766 1700 1 chr5B.!!$R2 934

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
532 589 0.394762 TCTGGCAATGTCTGGATGGC 60.395 55.0 0.0 0.0 39.81 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1894 2881 0.038166 AAAGACATGCCCATCGGTGT 59.962 50.0 0.0 0.0 0.0 4.16 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
35 36 5.355670 AGGGAGCCTAGATATGAAACCTA 57.644 43.478 0.00 0.00 28.47 3.08
36 37 5.727630 AGGGAGCCTAGATATGAAACCTAA 58.272 41.667 0.00 0.00 28.47 2.69
38 39 6.795000 AGGGAGCCTAGATATGAAACCTAAAT 59.205 38.462 0.00 0.00 28.47 1.40
50 51 9.936329 ATATGAAACCTAAATAATTGTGACCCT 57.064 29.630 0.00 0.00 0.00 4.34
51 52 8.664669 ATGAAACCTAAATAATTGTGACCCTT 57.335 30.769 0.00 0.00 0.00 3.95
52 53 8.117813 TGAAACCTAAATAATTGTGACCCTTC 57.882 34.615 0.00 0.00 0.00 3.46
53 54 7.947890 TGAAACCTAAATAATTGTGACCCTTCT 59.052 33.333 0.00 0.00 0.00 2.85
54 55 7.703058 AACCTAAATAATTGTGACCCTTCTG 57.297 36.000 0.00 0.00 0.00 3.02
66 67 4.092968 GTGACCCTTCTGCGTTTTATACAG 59.907 45.833 0.00 0.00 0.00 2.74
129 133 2.178764 TCCTCCTATCACTCTCATGGCT 59.821 50.000 0.00 0.00 0.00 4.75
137 141 6.204301 CCTATCACTCTCATGGCTTGTAAATG 59.796 42.308 0.00 0.00 0.00 2.32
142 146 6.257411 CACTCTCATGGCTTGTAAATGAGTAG 59.743 42.308 10.70 9.44 44.95 2.57
148 152 3.623510 GGCTTGTAAATGAGTAGCTGTCC 59.376 47.826 0.00 0.00 32.58 4.02
175 179 4.452455 AGTCAAATGGCTTCTCTTACGTTG 59.548 41.667 0.00 0.00 0.00 4.10
185 189 6.019479 GGCTTCTCTTACGTTGTGATTGATAG 60.019 42.308 0.00 0.00 0.00 2.08
187 191 7.275779 GCTTCTCTTACGTTGTGATTGATAGAA 59.724 37.037 0.00 0.00 0.00 2.10
188 192 9.140286 CTTCTCTTACGTTGTGATTGATAGAAA 57.860 33.333 0.00 0.00 0.00 2.52
189 193 9.483916 TTCTCTTACGTTGTGATTGATAGAAAA 57.516 29.630 0.00 0.00 0.00 2.29
191 195 9.746711 CTCTTACGTTGTGATTGATAGAAAAAG 57.253 33.333 0.00 0.00 0.00 2.27
192 196 9.268268 TCTTACGTTGTGATTGATAGAAAAAGT 57.732 29.630 0.00 0.00 0.00 2.66
193 197 9.318041 CTTACGTTGTGATTGATAGAAAAAGTG 57.682 33.333 0.00 0.00 0.00 3.16
194 198 7.490962 ACGTTGTGATTGATAGAAAAAGTGA 57.509 32.000 0.00 0.00 0.00 3.41
195 199 7.925993 ACGTTGTGATTGATAGAAAAAGTGAA 58.074 30.769 0.00 0.00 0.00 3.18
196 200 8.070171 ACGTTGTGATTGATAGAAAAAGTGAAG 58.930 33.333 0.00 0.00 0.00 3.02
237 241 2.137810 TGTAGCCTTTGGTTATGGCC 57.862 50.000 0.00 0.00 45.84 5.36
238 242 1.638589 TGTAGCCTTTGGTTATGGCCT 59.361 47.619 3.32 0.00 45.84 5.19
256 260 2.033550 GCCTAGAGTCACGTGACCTATG 59.966 54.545 38.00 30.88 45.85 2.23
257 261 3.280295 CCTAGAGTCACGTGACCTATGT 58.720 50.000 38.00 23.57 45.85 2.29
258 262 4.449131 CCTAGAGTCACGTGACCTATGTA 58.551 47.826 38.00 23.72 45.85 2.29
259 263 5.064558 CCTAGAGTCACGTGACCTATGTAT 58.935 45.833 38.00 22.18 45.85 2.29
260 264 5.179742 CCTAGAGTCACGTGACCTATGTATC 59.820 48.000 38.00 27.75 45.85 2.24
261 265 4.783055 AGAGTCACGTGACCTATGTATCT 58.217 43.478 38.00 29.23 45.85 1.98
286 290 1.672145 GCCTCGGACCTCTTGTTGTAC 60.672 57.143 0.00 0.00 0.00 2.90
291 295 2.417719 GGACCTCTTGTTGTACTGCAG 58.582 52.381 13.48 13.48 0.00 4.41
292 296 1.801178 GACCTCTTGTTGTACTGCAGC 59.199 52.381 15.27 0.00 0.00 5.25
294 298 1.605457 CCTCTTGTTGTACTGCAGCGA 60.605 52.381 15.27 0.00 0.00 4.93
322 329 3.058115 CCGTGTCAATGTCGGCATA 57.942 52.632 1.27 0.00 37.90 3.14
323 330 0.650512 CCGTGTCAATGTCGGCATAC 59.349 55.000 1.27 0.00 37.90 2.39
374 381 6.180472 AGAAACATATGGAAATCCGTTGAGT 58.820 36.000 7.80 0.00 39.43 3.41
378 385 6.852664 ACATATGGAAATCCGTTGAGTTTTC 58.147 36.000 7.80 0.00 39.43 2.29
383 390 2.270352 ATCCGTTGAGTTTTCTGGCA 57.730 45.000 0.00 0.00 0.00 4.92
392 399 2.260869 TTTTCTGGCAGCAGTCCGC 61.261 57.895 10.34 0.00 42.91 5.54
407 414 4.236935 CAGTCCGCTGCACAATAAAATTT 58.763 39.130 0.00 0.00 35.77 1.82
408 415 4.090354 CAGTCCGCTGCACAATAAAATTTG 59.910 41.667 0.00 0.00 35.77 2.32
415 422 5.284428 TGCACAATAAAATTTGCAGCATG 57.716 34.783 0.00 0.00 40.01 4.06
418 428 5.566016 GCACAATAAAATTTGCAGCATGTTG 59.434 36.000 5.00 5.00 39.31 3.33
423 433 8.473016 CAATAAAATTTGCAGCATGTTGTTTTG 58.527 29.630 11.44 0.00 39.31 2.44
432 442 4.155644 CAGCATGTTGTTTTGTTTTTGGGT 59.844 37.500 0.65 0.00 0.00 4.51
453 463 6.435904 TGGGTATAAAATTTGCAACAGCTAGT 59.564 34.615 0.00 0.00 0.00 2.57
465 475 3.971032 ACAGCTAGTTGAACACTTTGC 57.029 42.857 14.09 0.00 36.88 3.68
472 482 4.292977 AGTTGAACACTTTGCAAGCTAC 57.707 40.909 0.00 0.00 27.32 3.58
473 483 3.035942 GTTGAACACTTTGCAAGCTACG 58.964 45.455 0.00 0.00 0.00 3.51
475 485 3.459145 TGAACACTTTGCAAGCTACGTA 58.541 40.909 0.00 0.00 0.00 3.57
476 486 3.872182 TGAACACTTTGCAAGCTACGTAA 59.128 39.130 0.00 0.00 0.00 3.18
477 487 4.513692 TGAACACTTTGCAAGCTACGTAAT 59.486 37.500 0.00 0.00 0.00 1.89
478 488 5.008217 TGAACACTTTGCAAGCTACGTAATT 59.992 36.000 0.00 0.00 0.00 1.40
479 489 4.783242 ACACTTTGCAAGCTACGTAATTG 58.217 39.130 13.32 13.32 0.00 2.32
517 572 2.277373 GACGCGACGCTAGTCTGG 60.277 66.667 15.93 2.48 44.93 3.86
532 589 0.394762 TCTGGCAATGTCTGGATGGC 60.395 55.000 0.00 0.00 39.81 4.40
535 592 1.284491 TGGCAATGTCTGGATGGCTAA 59.716 47.619 0.00 0.00 40.04 3.09
536 593 2.091720 TGGCAATGTCTGGATGGCTAAT 60.092 45.455 0.00 0.00 40.04 1.73
538 595 2.295349 GCAATGTCTGGATGGCTAATGG 59.705 50.000 0.00 0.00 0.00 3.16
539 596 2.889045 CAATGTCTGGATGGCTAATGGG 59.111 50.000 0.00 0.00 0.00 4.00
540 597 1.595311 TGTCTGGATGGCTAATGGGT 58.405 50.000 0.00 0.00 0.00 4.51
566 623 6.858478 AGAAATGTCGACGATGATACATGTAG 59.142 38.462 11.91 0.00 33.04 2.74
589 646 4.213694 GTCGATTGAGGACGAGCTAATAGA 59.786 45.833 0.00 0.00 39.16 1.98
604 661 5.817816 AGCTAATAGATCTTGTTTGGAACGG 59.182 40.000 0.00 0.00 0.00 4.44
612 669 1.021202 TGTTTGGAACGGAAGCACAG 58.979 50.000 0.00 0.00 0.00 3.66
623 680 3.632145 ACGGAAGCACAGAGAACAAAAAT 59.368 39.130 0.00 0.00 0.00 1.82
629 686 4.816385 AGCACAGAGAACAAAAATTCGAGA 59.184 37.500 0.00 0.00 33.57 4.04
795 875 6.395629 TCTGACTTTCGACCACCTAAATAAG 58.604 40.000 0.00 0.00 0.00 1.73
800 880 8.315391 ACTTTCGACCACCTAAATAAGTTAAC 57.685 34.615 0.00 0.00 0.00 2.01
923 1028 1.499438 TCCGTACTCCATCTCTCCCAT 59.501 52.381 0.00 0.00 0.00 4.00
926 1031 2.753168 CGTACTCCATCTCTCCCATCCA 60.753 54.545 0.00 0.00 0.00 3.41
927 1032 2.811322 ACTCCATCTCTCCCATCCAT 57.189 50.000 0.00 0.00 0.00 3.41
928 1033 2.618794 ACTCCATCTCTCCCATCCATC 58.381 52.381 0.00 0.00 0.00 3.51
929 1034 2.090324 ACTCCATCTCTCCCATCCATCA 60.090 50.000 0.00 0.00 0.00 3.07
935 1051 2.918934 TCTCTCCCATCCATCAAAACCA 59.081 45.455 0.00 0.00 0.00 3.67
1017 1147 2.758327 ATGGCACGGTCGGAGCTA 60.758 61.111 5.58 4.78 0.00 3.32
1152 1282 2.564975 CAAGGTACGTCCGTCGCT 59.435 61.111 0.00 0.00 44.19 4.93
1162 1566 1.401018 CGTCCGTCGCTATATGCATCA 60.401 52.381 0.19 0.00 43.06 3.07
1197 1607 1.583054 ACAAGACAGAGCGGAAACAC 58.417 50.000 0.00 0.00 0.00 3.32
1209 1620 2.603560 GCGGAAACACGGATCTTCTTAG 59.396 50.000 0.00 0.00 0.00 2.18
1230 2015 5.945775 AGCGCTAACGACTAAATTAACTC 57.054 39.130 8.99 0.00 43.93 3.01
1238 2023 7.611213 AACGACTAAATTAACTCATCCTTGG 57.389 36.000 0.00 0.00 0.00 3.61
1787 2767 4.201456 CGTACGCACAATTGTACTGTACTG 60.201 45.833 27.05 21.11 38.99 2.74
1805 2792 6.387465 TGTACTGTATGTAAGAGAGTGTTGC 58.613 40.000 0.00 0.00 32.25 4.17
1830 2817 5.067283 TGTTCCCTTTTTCTTTTTCGGAGAG 59.933 40.000 0.00 0.00 38.43 3.20
1868 2855 9.889128 ATTGGTTATGTTGATATTGGGAAAAAG 57.111 29.630 0.00 0.00 0.00 2.27
1869 2856 7.846066 TGGTTATGTTGATATTGGGAAAAAGG 58.154 34.615 0.00 0.00 0.00 3.11
1870 2857 7.676043 TGGTTATGTTGATATTGGGAAAAAGGA 59.324 33.333 0.00 0.00 0.00 3.36
1871 2858 8.536175 GGTTATGTTGATATTGGGAAAAAGGAA 58.464 33.333 0.00 0.00 0.00 3.36
1872 2859 9.936759 GTTATGTTGATATTGGGAAAAAGGAAA 57.063 29.630 0.00 0.00 0.00 3.13
1913 2900 0.038166 ACACCGATGGGCATGTCTTT 59.962 50.000 0.00 0.00 36.48 2.52
1914 2901 1.280710 ACACCGATGGGCATGTCTTTA 59.719 47.619 0.00 0.00 36.48 1.85
1915 2902 1.942657 CACCGATGGGCATGTCTTTAG 59.057 52.381 0.00 0.00 36.48 1.85
1917 2904 1.140852 CCGATGGGCATGTCTTTAGGA 59.859 52.381 0.00 0.00 0.00 2.94
1919 2906 2.614057 CGATGGGCATGTCTTTAGGAAC 59.386 50.000 0.00 0.00 0.00 3.62
1920 2907 3.620488 GATGGGCATGTCTTTAGGAACA 58.380 45.455 0.00 0.00 0.00 3.18
1922 2909 3.838565 TGGGCATGTCTTTAGGAACAAA 58.161 40.909 0.00 0.00 0.00 2.83
1923 2910 4.219115 TGGGCATGTCTTTAGGAACAAAA 58.781 39.130 0.00 0.00 0.00 2.44
1924 2911 4.651503 TGGGCATGTCTTTAGGAACAAAAA 59.348 37.500 0.00 0.00 0.00 1.94
1925 2912 4.988540 GGGCATGTCTTTAGGAACAAAAAC 59.011 41.667 0.00 0.00 0.00 2.43
1926 2913 4.679654 GGCATGTCTTTAGGAACAAAAACG 59.320 41.667 0.00 0.00 0.00 3.60
1927 2914 4.679654 GCATGTCTTTAGGAACAAAAACGG 59.320 41.667 0.00 0.00 0.00 4.44
1928 2915 5.506649 GCATGTCTTTAGGAACAAAAACGGA 60.507 40.000 0.00 0.00 0.00 4.69
1938 2925 4.498513 GGAACAAAAACGGAGAAAACGGAT 60.499 41.667 0.00 0.00 35.23 4.18
2016 3018 8.601845 AAAACAAATACATAAACAAAGAGCCC 57.398 30.769 0.00 0.00 0.00 5.19
2037 3039 2.508526 GTTCTTGTCTGGGTCAAGCAT 58.491 47.619 0.00 0.00 41.13 3.79
2073 3076 6.847956 TCAAAAGATTTGCCACTTTCATTG 57.152 33.333 0.00 0.00 35.66 2.82
2080 3083 5.606348 TTTGCCACTTTCATTGGTTAAGT 57.394 34.783 0.00 0.00 36.40 2.24
2090 3107 0.320073 TTGGTTAAGTGAGACCCGCG 60.320 55.000 0.00 0.00 34.99 6.46
2133 3156 2.198406 TCTCGCGGCATTACATTACAC 58.802 47.619 6.13 0.00 0.00 2.90
2139 3162 4.667262 GCGGCATTACATTACACAAATGA 58.333 39.130 4.82 0.00 46.81 2.57
2140 3163 5.280945 GCGGCATTACATTACACAAATGAT 58.719 37.500 4.82 0.00 46.81 2.45
2141 3164 5.173673 GCGGCATTACATTACACAAATGATG 59.826 40.000 4.82 1.10 46.81 3.07
2143 3166 6.634035 CGGCATTACATTACACAAATGATGAG 59.366 38.462 4.82 0.00 46.81 2.90
2144 3167 6.418819 GGCATTACATTACACAAATGATGAGC 59.581 38.462 4.82 3.94 46.81 4.26
2145 3168 6.974048 GCATTACATTACACAAATGATGAGCA 59.026 34.615 4.82 0.00 46.81 4.26
2146 3169 7.043854 GCATTACATTACACAAATGATGAGCAC 60.044 37.037 4.82 0.00 46.81 4.40
2147 3170 5.314923 ACATTACACAAATGATGAGCACC 57.685 39.130 4.82 0.00 46.81 5.01
2148 3171 4.158394 ACATTACACAAATGATGAGCACCC 59.842 41.667 4.82 0.00 46.81 4.61
2149 3172 1.549203 ACACAAATGATGAGCACCCC 58.451 50.000 0.00 0.00 0.00 4.95
2150 3173 1.203038 ACACAAATGATGAGCACCCCA 60.203 47.619 0.00 0.00 0.00 4.96
2151 3174 1.203052 CACAAATGATGAGCACCCCAC 59.797 52.381 0.00 0.00 0.00 4.61
2152 3175 1.203038 ACAAATGATGAGCACCCCACA 60.203 47.619 0.00 0.00 0.00 4.17
2153 3176 1.894466 CAAATGATGAGCACCCCACAA 59.106 47.619 0.00 0.00 0.00 3.33
2154 3177 1.843368 AATGATGAGCACCCCACAAG 58.157 50.000 0.00 0.00 0.00 3.16
2184 3207 0.990818 AGGGCCTCCTCTTTGATCCC 60.991 60.000 0.00 0.00 39.80 3.85
2185 3208 1.534203 GGCCTCCTCTTTGATCCCC 59.466 63.158 0.00 0.00 0.00 4.81
2232 3255 5.963586 CGACGGTATTCCTAAAAATTCTTGC 59.036 40.000 0.00 0.00 0.00 4.01
2250 3273 4.217334 TCTTGCGTTATGCTCATTCCAAAA 59.783 37.500 0.00 0.00 46.63 2.44
2267 3290 2.695147 CAAAACTCCCAGGAAACAAGCT 59.305 45.455 0.00 0.00 0.00 3.74
2323 3347 3.209410 CCTATCCAAGACAGCCATGAAC 58.791 50.000 0.00 0.00 0.00 3.18
2345 3370 2.040178 ACAAGTCTTGACCGAGACCTT 58.960 47.619 19.53 5.45 45.69 3.50
2386 3411 1.278985 TGCCATTGTTGAGACCGATCT 59.721 47.619 0.00 0.00 38.15 2.75
2399 3424 2.292569 GACCGATCTACGAAGCCACATA 59.707 50.000 0.00 0.00 45.77 2.29
2466 3491 4.201910 GGCGCAGATTCATTAACTTGCTTA 60.202 41.667 10.83 0.00 0.00 3.09
2526 3551 4.740822 AGCCGGCCAACCATCCAC 62.741 66.667 26.15 0.00 34.57 4.02
2591 3616 0.393132 GGTGCCCAAGCCTTCTAGAC 60.393 60.000 0.00 0.00 38.69 2.59
2593 3618 1.153349 GCCCAAGCCTTCTAGACGG 60.153 63.158 10.92 10.92 0.00 4.79
2596 3621 0.179134 CCAAGCCTTCTAGACGGACG 60.179 60.000 19.09 5.85 0.00 4.79
2608 3633 1.772063 GACGGACGTGGGCATATTGC 61.772 60.000 0.53 0.00 44.08 3.56
2616 3641 2.164219 CGTGGGCATATTGCTTTTGAGT 59.836 45.455 0.00 0.00 44.28 3.41
2625 3650 1.604604 TGCTTTTGAGTTTCCCCTCG 58.395 50.000 0.00 0.00 34.04 4.63
2628 3653 2.031069 GCTTTTGAGTTTCCCCTCGAAC 60.031 50.000 0.00 0.00 35.15 3.95
2629 3654 2.265589 TTTGAGTTTCCCCTCGAACC 57.734 50.000 0.00 0.00 31.34 3.62
2641 3666 0.806102 CTCGAACCGTGCCATGTAGG 60.806 60.000 0.00 0.00 41.84 3.18
2693 3718 5.542779 AGTGAGTTTCCAACAGATAGTGTC 58.457 41.667 0.00 0.00 39.03 3.67
2697 3722 3.313012 TTCCAACAGATAGTGTCACGG 57.687 47.619 0.00 0.00 39.03 4.94
2698 3723 1.548719 TCCAACAGATAGTGTCACGGG 59.451 52.381 0.00 0.00 39.03 5.28
2699 3724 1.359848 CAACAGATAGTGTCACGGGC 58.640 55.000 0.00 0.00 39.03 6.13
2700 3725 0.108804 AACAGATAGTGTCACGGGCG 60.109 55.000 0.00 0.00 39.03 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.359459 GCTCCCTTTGGACTTACGCG 61.359 60.000 3.53 3.53 35.03 6.01
1 2 1.025113 GGCTCCCTTTGGACTTACGC 61.025 60.000 0.00 0.00 35.03 4.42
3 4 3.105283 TCTAGGCTCCCTTTGGACTTAC 58.895 50.000 0.00 0.00 35.03 2.34
4 5 3.484953 TCTAGGCTCCCTTTGGACTTA 57.515 47.619 0.00 0.00 35.03 2.24
6 7 2.577772 ATCTAGGCTCCCTTTGGACT 57.422 50.000 0.00 0.00 35.03 3.85
7 8 3.904339 TCATATCTAGGCTCCCTTTGGAC 59.096 47.826 0.00 0.00 35.03 4.02
35 36 4.079253 ACGCAGAAGGGTCACAATTATTT 58.921 39.130 0.00 0.00 35.88 1.40
36 37 3.686016 ACGCAGAAGGGTCACAATTATT 58.314 40.909 0.00 0.00 35.88 1.40
38 39 2.851263 ACGCAGAAGGGTCACAATTA 57.149 45.000 0.00 0.00 35.88 1.40
44 45 4.250464 CTGTATAAAACGCAGAAGGGTCA 58.750 43.478 0.00 0.00 40.41 4.02
45 46 4.251268 ACTGTATAAAACGCAGAAGGGTC 58.749 43.478 0.00 0.00 40.41 4.46
47 48 4.935808 AGAACTGTATAAAACGCAGAAGGG 59.064 41.667 0.00 0.00 34.60 3.95
48 49 6.307155 CAAGAACTGTATAAAACGCAGAAGG 58.693 40.000 0.00 0.00 34.60 3.46
49 50 5.790495 GCAAGAACTGTATAAAACGCAGAAG 59.210 40.000 0.00 0.00 34.60 2.85
50 51 5.468746 AGCAAGAACTGTATAAAACGCAGAA 59.531 36.000 0.00 0.00 34.60 3.02
51 52 4.994852 AGCAAGAACTGTATAAAACGCAGA 59.005 37.500 0.00 0.00 34.60 4.26
52 53 5.082059 CAGCAAGAACTGTATAAAACGCAG 58.918 41.667 0.00 0.00 36.41 5.18
53 54 5.029650 CAGCAAGAACTGTATAAAACGCA 57.970 39.130 0.00 0.00 32.78 5.24
66 67 2.494059 TCAACCTAGCACAGCAAGAAC 58.506 47.619 0.00 0.00 0.00 3.01
129 133 5.222079 TGTGGACAGCTACTCATTTACAA 57.778 39.130 0.00 0.00 0.00 2.41
137 141 3.386768 TTGACTTGTGGACAGCTACTC 57.613 47.619 0.00 0.00 0.00 2.59
142 146 1.336240 GCCATTTGACTTGTGGACAGC 60.336 52.381 0.00 0.00 34.94 4.40
148 152 4.843220 AAGAGAAGCCATTTGACTTGTG 57.157 40.909 0.00 0.00 0.00 3.33
175 179 8.099364 TCACCTTCACTTTTTCTATCAATCAC 57.901 34.615 0.00 0.00 0.00 3.06
185 189 8.490355 CATTATTTGCTTCACCTTCACTTTTTC 58.510 33.333 0.00 0.00 0.00 2.29
187 191 7.951530 CATTATTTGCTTCACCTTCACTTTT 57.048 32.000 0.00 0.00 0.00 2.27
237 241 5.992829 AGATACATAGGTCACGTGACTCTAG 59.007 44.000 39.01 28.98 44.20 2.43
238 242 5.758784 CAGATACATAGGTCACGTGACTCTA 59.241 44.000 39.01 34.55 44.20 2.43
256 260 2.229302 GAGGTCCGAGGCATACAGATAC 59.771 54.545 0.00 0.00 0.00 2.24
257 261 2.108425 AGAGGTCCGAGGCATACAGATA 59.892 50.000 0.00 0.00 0.00 1.98
258 262 1.133325 AGAGGTCCGAGGCATACAGAT 60.133 52.381 0.00 0.00 0.00 2.90
259 263 0.259065 AGAGGTCCGAGGCATACAGA 59.741 55.000 0.00 0.00 0.00 3.41
260 264 1.115467 AAGAGGTCCGAGGCATACAG 58.885 55.000 0.00 0.00 0.00 2.74
261 265 0.824109 CAAGAGGTCCGAGGCATACA 59.176 55.000 0.00 0.00 0.00 2.29
291 295 0.163146 GACACGGCAGTTAAAGTCGC 59.837 55.000 3.40 0.00 37.67 5.19
292 296 1.493772 TGACACGGCAGTTAAAGTCG 58.506 50.000 2.06 2.06 40.47 4.18
294 298 3.211045 ACATTGACACGGCAGTTAAAGT 58.789 40.909 0.00 0.00 0.00 2.66
322 329 5.931146 TGTTGAATTTGTTGACAGCAAAAGT 59.069 32.000 19.44 11.61 38.98 2.66
323 330 6.406093 TGTTGAATTTGTTGACAGCAAAAG 57.594 33.333 19.44 0.00 38.98 2.27
374 381 2.260869 GCGGACTGCTGCCAGAAAA 61.261 57.895 0.00 0.00 41.77 2.29
407 414 4.379186 CCAAAAACAAAACAACATGCTGCA 60.379 37.500 4.13 4.13 0.00 4.41
408 415 4.097012 CCAAAAACAAAACAACATGCTGC 58.903 39.130 0.00 0.00 0.00 5.25
411 418 4.693538 ACCCAAAAACAAAACAACATGC 57.306 36.364 0.00 0.00 0.00 4.06
418 428 9.788960 TGCAAATTTTATACCCAAAAACAAAAC 57.211 25.926 0.00 0.00 31.54 2.43
423 433 7.589587 GCTGTTGCAAATTTTATACCCAAAAAC 59.410 33.333 0.00 0.00 39.41 2.43
465 475 4.085055 CCGACTATGCAATTACGTAGCTTG 60.085 45.833 12.96 12.96 33.24 4.01
472 482 1.070577 GCAGCCGACTATGCAATTACG 60.071 52.381 0.00 0.00 42.11 3.18
473 483 1.264288 GGCAGCCGACTATGCAATTAC 59.736 52.381 0.00 0.00 44.37 1.89
475 485 0.394216 TGGCAGCCGACTATGCAATT 60.394 50.000 7.03 0.00 44.37 2.32
476 486 1.097547 GTGGCAGCCGACTATGCAAT 61.098 55.000 7.03 0.00 44.37 3.56
477 487 1.745115 GTGGCAGCCGACTATGCAA 60.745 57.895 7.03 0.00 44.37 4.08
478 488 2.125147 GTGGCAGCCGACTATGCA 60.125 61.111 7.03 0.00 44.37 3.96
479 489 1.884926 GAGTGGCAGCCGACTATGC 60.885 63.158 14.41 2.27 41.80 3.14
517 572 2.295349 CCATTAGCCATCCAGACATTGC 59.705 50.000 0.00 0.00 0.00 3.56
532 589 4.928601 TCGTCGACATTTCTACCCATTAG 58.071 43.478 17.16 0.00 0.00 1.73
535 592 3.383505 TCATCGTCGACATTTCTACCCAT 59.616 43.478 17.16 0.00 0.00 4.00
536 593 2.756207 TCATCGTCGACATTTCTACCCA 59.244 45.455 17.16 0.00 0.00 4.51
538 595 5.516996 TGTATCATCGTCGACATTTCTACC 58.483 41.667 17.16 0.00 0.00 3.18
539 596 6.637254 ACATGTATCATCGTCGACATTTCTAC 59.363 38.462 17.16 11.20 30.13 2.59
540 597 6.735130 ACATGTATCATCGTCGACATTTCTA 58.265 36.000 17.16 0.00 30.13 2.10
566 623 2.846039 TTAGCTCGTCCTCAATCGAC 57.154 50.000 0.00 0.00 32.65 4.20
571 628 5.594725 ACAAGATCTATTAGCTCGTCCTCAA 59.405 40.000 0.00 0.00 0.00 3.02
589 646 2.293399 GTGCTTCCGTTCCAAACAAGAT 59.707 45.455 0.00 0.00 0.00 2.40
604 661 5.510671 TCGAATTTTTGTTCTCTGTGCTTC 58.489 37.500 0.00 0.00 0.00 3.86
623 680 8.110860 AGCTAATTCTTGGAAAATTTCTCGAA 57.889 30.769 5.65 6.53 0.00 3.71
636 693 8.831550 GGAGTAATTAACTGAGCTAATTCTTGG 58.168 37.037 4.28 0.00 39.07 3.61
762 836 4.339530 TGGTCGAAAGTCAGATCATCTAGG 59.660 45.833 0.00 0.00 0.00 3.02
795 875 6.260271 GGCACCCATCTGATTAACTAGTTAAC 59.740 42.308 26.34 19.99 37.80 2.01
923 1028 0.671251 GTTGCGGTGGTTTTGATGGA 59.329 50.000 0.00 0.00 0.00 3.41
926 1031 1.339929 GAAGGTTGCGGTGGTTTTGAT 59.660 47.619 0.00 0.00 0.00 2.57
927 1032 0.741915 GAAGGTTGCGGTGGTTTTGA 59.258 50.000 0.00 0.00 0.00 2.69
928 1033 0.744281 AGAAGGTTGCGGTGGTTTTG 59.256 50.000 0.00 0.00 0.00 2.44
929 1034 1.029681 GAGAAGGTTGCGGTGGTTTT 58.970 50.000 0.00 0.00 0.00 2.43
935 1051 1.371558 GGTCAGAGAAGGTTGCGGT 59.628 57.895 0.00 0.00 0.00 5.68
1017 1147 4.704833 ACCAGCAACGCCATCGCT 62.705 61.111 0.00 0.00 39.84 4.93
1020 1150 2.672996 ACCACCAGCAACGCCATC 60.673 61.111 0.00 0.00 0.00 3.51
1152 1282 4.064388 CACCAATCCGTGTGATGCATATA 58.936 43.478 0.00 0.00 34.37 0.86
1197 1607 2.044860 CGTTAGCGCTAAGAAGATCCG 58.955 52.381 29.42 21.94 0.00 4.18
1209 1620 5.691508 TGAGTTAATTTAGTCGTTAGCGC 57.308 39.130 0.00 0.00 38.14 5.92
1230 2015 1.815003 GTGAAGAACTGGCCAAGGATG 59.185 52.381 7.01 0.00 0.00 3.51
1238 2023 3.423154 CCGGCGTGAAGAACTGGC 61.423 66.667 6.01 0.00 0.00 4.85
1458 2258 4.814294 GACGCGGTACTGGGCCTG 62.814 72.222 18.06 9.11 0.00 4.85
1464 2267 4.849329 GAGGGCGACGCGGTACTG 62.849 72.222 14.61 0.00 0.00 2.74
1628 2431 0.744874 CGGAGAAGGCGGAGAATACA 59.255 55.000 0.00 0.00 0.00 2.29
1787 2767 5.348997 GGAACAGCAACACTCTCTTACATAC 59.651 44.000 0.00 0.00 0.00 2.39
1805 2792 5.067283 TCTCCGAAAAAGAAAAAGGGAACAG 59.933 40.000 0.00 0.00 0.00 3.16
1873 2860 9.413048 CGGTGTTATTACAACATAACCAAATTT 57.587 29.630 0.26 0.00 42.30 1.82
1874 2861 8.794553 TCGGTGTTATTACAACATAACCAAATT 58.205 29.630 0.26 0.00 42.30 1.82
1875 2862 8.338072 TCGGTGTTATTACAACATAACCAAAT 57.662 30.769 0.26 0.00 42.30 2.32
1876 2863 7.741027 TCGGTGTTATTACAACATAACCAAA 57.259 32.000 0.26 0.00 42.30 3.28
1877 2864 7.148222 CCATCGGTGTTATTACAACATAACCAA 60.148 37.037 0.26 0.00 42.30 3.67
1878 2865 6.316640 CCATCGGTGTTATTACAACATAACCA 59.683 38.462 0.26 0.00 42.30 3.67
1879 2866 6.238538 CCCATCGGTGTTATTACAACATAACC 60.239 42.308 0.26 0.00 42.30 2.85
1880 2867 6.721321 CCCATCGGTGTTATTACAACATAAC 58.279 40.000 0.26 0.00 42.30 1.89
1881 2868 5.297278 GCCCATCGGTGTTATTACAACATAA 59.703 40.000 0.26 0.00 42.30 1.90
1882 2869 4.817464 GCCCATCGGTGTTATTACAACATA 59.183 41.667 0.26 0.00 42.30 2.29
1883 2870 3.630312 GCCCATCGGTGTTATTACAACAT 59.370 43.478 0.26 0.00 42.30 2.71
1884 2871 3.011119 GCCCATCGGTGTTATTACAACA 58.989 45.455 0.26 0.00 42.30 3.33
1885 2872 3.011119 TGCCCATCGGTGTTATTACAAC 58.989 45.455 0.00 0.00 38.66 3.32
1886 2873 3.351794 TGCCCATCGGTGTTATTACAA 57.648 42.857 0.00 0.00 35.69 2.41
1887 2874 3.210227 CATGCCCATCGGTGTTATTACA 58.790 45.455 0.00 0.00 0.00 2.41
1888 2875 3.211045 ACATGCCCATCGGTGTTATTAC 58.789 45.455 0.00 0.00 0.00 1.89
1894 2881 0.038166 AAAGACATGCCCATCGGTGT 59.962 50.000 0.00 0.00 0.00 4.16
1913 2900 4.035441 CCGTTTTCTCCGTTTTTGTTCCTA 59.965 41.667 0.00 0.00 0.00 2.94
1914 2901 3.181494 CCGTTTTCTCCGTTTTTGTTCCT 60.181 43.478 0.00 0.00 0.00 3.36
1915 2902 3.110358 CCGTTTTCTCCGTTTTTGTTCC 58.890 45.455 0.00 0.00 0.00 3.62
1917 2904 4.096682 TCATCCGTTTTCTCCGTTTTTGTT 59.903 37.500 0.00 0.00 0.00 2.83
1919 2906 4.217754 TCATCCGTTTTCTCCGTTTTTG 57.782 40.909 0.00 0.00 0.00 2.44
1920 2907 3.881089 ACTCATCCGTTTTCTCCGTTTTT 59.119 39.130 0.00 0.00 0.00 1.94
1922 2909 3.121738 ACTCATCCGTTTTCTCCGTTT 57.878 42.857 0.00 0.00 0.00 3.60
1923 2910 2.833631 ACTCATCCGTTTTCTCCGTT 57.166 45.000 0.00 0.00 0.00 4.44
1924 2911 2.299297 AGAACTCATCCGTTTTCTCCGT 59.701 45.455 0.00 0.00 0.00 4.69
1925 2912 2.960819 AGAACTCATCCGTTTTCTCCG 58.039 47.619 0.00 0.00 0.00 4.63
1926 2913 4.152580 GTGAAGAACTCATCCGTTTTCTCC 59.847 45.833 0.00 0.00 36.14 3.71
1927 2914 4.750098 TGTGAAGAACTCATCCGTTTTCTC 59.250 41.667 0.00 0.00 36.14 2.87
1928 2915 4.703897 TGTGAAGAACTCATCCGTTTTCT 58.296 39.130 0.00 0.00 36.14 2.52
1938 2925 8.006298 ACCATAAAACAAATGTGAAGAACTCA 57.994 30.769 0.00 0.00 0.00 3.41
2016 3018 0.868406 GCTTGACCCAGACAAGAACG 59.132 55.000 10.29 0.00 44.92 3.95
2045 3047 8.278729 TGAAAGTGGCAAATCTTTTGAAATTT 57.721 26.923 4.24 0.00 34.60 1.82
2046 3048 7.862512 TGAAAGTGGCAAATCTTTTGAAATT 57.137 28.000 4.24 0.00 34.60 1.82
2047 3049 8.347035 CAATGAAAGTGGCAAATCTTTTGAAAT 58.653 29.630 4.24 0.00 34.60 2.17
2065 3068 4.154195 CGGGTCTCACTTAACCAATGAAAG 59.846 45.833 0.00 0.00 37.28 2.62
2073 3076 0.458025 CTCGCGGGTCTCACTTAACC 60.458 60.000 6.13 0.00 34.64 2.85
2090 3107 1.381463 ACTCTCTTACCCCCGCCTC 60.381 63.158 0.00 0.00 0.00 4.70
2121 3144 7.433131 GGTGCTCATCATTTGTGTAATGTAATG 59.567 37.037 0.00 0.00 43.41 1.90
2133 3156 1.548081 TGTGGGGTGCTCATCATTTG 58.452 50.000 0.00 0.00 0.00 2.32
2138 3161 2.401766 CGCTTGTGGGGTGCTCATC 61.402 63.158 0.00 0.00 0.00 2.92
2139 3162 2.360350 CGCTTGTGGGGTGCTCAT 60.360 61.111 0.00 0.00 0.00 2.90
2145 3168 4.531426 TTTGGGCGCTTGTGGGGT 62.531 61.111 7.64 0.00 0.00 4.95
2146 3169 2.801631 TTTTTGGGCGCTTGTGGGG 61.802 57.895 7.64 0.00 0.00 4.96
2147 3170 2.818132 TTTTTGGGCGCTTGTGGG 59.182 55.556 7.64 0.00 0.00 4.61
2172 3195 1.682451 TACCGCGGGGATCAAAGAGG 61.682 60.000 31.76 0.00 36.97 3.69
2184 3207 3.086309 CGACCATTGTTACCGCGG 58.914 61.111 26.86 26.86 0.00 6.46
2185 3208 2.398036 GCGACCATTGTTACCGCG 59.602 61.111 0.00 0.00 36.53 6.46
2232 3255 4.438744 GGGAGTTTTGGAATGAGCATAACG 60.439 45.833 0.00 0.00 0.00 3.18
2250 3273 1.986882 CAAGCTTGTTTCCTGGGAGT 58.013 50.000 18.65 0.00 0.00 3.85
2267 3290 1.455849 CCCTCACCTCCTTGTGCAA 59.544 57.895 0.00 0.00 36.17 4.08
2310 3334 1.143684 ACTTGTGGTTCATGGCTGTCT 59.856 47.619 0.00 0.00 0.00 3.41
2315 3339 2.030805 GTCAAGACTTGTGGTTCATGGC 60.031 50.000 14.75 0.00 0.00 4.40
2316 3340 2.554032 GGTCAAGACTTGTGGTTCATGG 59.446 50.000 14.75 0.00 0.00 3.66
2323 3347 1.605712 GGTCTCGGTCAAGACTTGTGG 60.606 57.143 14.75 5.94 44.21 4.17
2368 3393 3.116300 CGTAGATCGGTCTCAACAATGG 58.884 50.000 0.00 0.00 35.87 3.16
2386 3411 1.268066 TGGGTGTATGTGGCTTCGTA 58.732 50.000 0.00 0.00 0.00 3.43
2515 3540 0.178964 AACTGGGTGTGGATGGTTGG 60.179 55.000 0.00 0.00 0.00 3.77
2518 3543 1.703411 CAAAACTGGGTGTGGATGGT 58.297 50.000 0.00 0.00 0.00 3.55
2524 3549 5.394115 GGCTAATTATCCAAAACTGGGTGTG 60.394 44.000 0.31 0.00 0.00 3.82
2526 3551 4.709397 TGGCTAATTATCCAAAACTGGGTG 59.291 41.667 5.56 0.00 0.00 4.61
2547 3572 0.947244 AGTGCAAGTTCTTCGCTTGG 59.053 50.000 7.09 0.00 42.44 3.61
2576 3601 0.175989 GTCCGTCTAGAAGGCTTGGG 59.824 60.000 18.93 1.23 0.00 4.12
2577 3602 0.179134 CGTCCGTCTAGAAGGCTTGG 60.179 60.000 18.93 0.00 0.00 3.61
2591 3616 1.095228 AAGCAATATGCCCACGTCCG 61.095 55.000 0.00 0.00 46.52 4.79
2593 3618 2.163412 TCAAAAGCAATATGCCCACGTC 59.837 45.455 0.00 0.00 46.52 4.34
2596 3621 3.874392 ACTCAAAAGCAATATGCCCAC 57.126 42.857 0.00 0.00 46.52 4.61
2608 3633 2.552743 GGTTCGAGGGGAAACTCAAAAG 59.447 50.000 0.00 0.00 39.36 2.27
2616 3641 2.031465 GCACGGTTCGAGGGGAAA 59.969 61.111 0.00 0.00 36.14 3.13
2641 3666 2.605366 GCGAGTACTCATCTTCTTTGGC 59.395 50.000 22.37 9.61 0.00 4.52
2676 3701 3.556213 CCCGTGACACTATCTGTTGGAAA 60.556 47.826 3.68 0.00 31.03 3.13
2679 3704 2.007049 GCCCGTGACACTATCTGTTGG 61.007 57.143 3.68 0.00 31.03 3.77


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

AutoCloner maintained by Alex Coulton.