Multiple sequence alignment - TraesCS3B01G541600

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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 TraesCS3B01G541600 chr3B 100.000 2297 0 0 1 2297 779647052 779644756 0.000000e+00 4242
1 TraesCS3B01G541600 chr3B 87.735 1753 166 23 582 2297 779694533 779692793 0.000000e+00 2001
2 TraesCS3B01G541600 chr3B 87.221 1745 183 14 586 2297 779714542 779712805 0.000000e+00 1951
3 TraesCS3B01G541600 chr3B 87.172 1754 177 22 582 2297 780061451 780059708 0.000000e+00 1949
4 TraesCS3B01G541600 chr3B 87.130 1756 175 24 582 2297 780090468 780088724 0.000000e+00 1943
5 TraesCS3B01G541600 chr3B 87.435 1337 149 10 974 2297 779989590 779988260 0.000000e+00 1520
6 TraesCS3B01G541600 chr3B 87.391 690 71 9 1619 2297 779975000 779974316 0.000000e+00 778
7 TraesCS3B01G541600 chr3B 100.000 363 0 0 2542 2904 779644511 779644149 0.000000e+00 671
8 TraesCS3B01G541600 chr3B 84.602 578 67 7 9 581 779997883 779997323 3.270000e-154 555
9 TraesCS3B01G541600 chr3B 84.602 578 65 9 9 581 780125951 780125393 1.180000e-153 553
10 TraesCS3B01G541600 chr3B 83.592 579 71 8 9 581 779941790 779941230 3.320000e-144 521
11 TraesCS3B01G541600 chr3B 86.024 415 45 4 1894 2297 779813272 779812860 1.600000e-117 433
12 TraesCS3B01G541600 chr3B 85.096 416 46 8 1894 2297 779816011 779815600 7.490000e-111 411
13 TraesCS3B01G541600 chr3B 82.729 469 55 8 586 1032 779819768 779819304 7.540000e-106 394
14 TraesCS3B01G541600 chr3B 89.316 234 20 2 2545 2773 779700821 779700588 3.660000e-74 289
15 TraesCS3B01G541600 chr3B 91.053 190 12 3 2587 2771 779812802 779812613 4.800000e-63 252
16 TraesCS3B01G541600 chr3B 91.053 190 12 3 2587 2771 779818284 779818095 4.800000e-63 252
17 TraesCS3B01G541600 chr3B 90.526 190 13 3 2587 2771 779988202 779988013 2.240000e-61 246
18 TraesCS3B01G541600 chr3B 89.583 192 15 3 2585 2771 779712749 779712558 3.740000e-59 239
19 TraesCS3B01G541600 chr3B 85.837 233 23 5 582 812 779963381 779963157 3.740000e-59 239
20 TraesCS3B01G541600 chr3B 74.866 374 50 26 2543 2904 779677716 779677375 2.350000e-26 130
21 TraesCS3B01G541600 chr3D 88.023 1553 147 14 781 2297 583001614 583000065 0.000000e+00 1801
22 TraesCS3B01G541600 chr3D 85.152 1549 170 37 778 2297 582899808 582898291 0.000000e+00 1531
23 TraesCS3B01G541600 chr3D 89.491 1199 99 8 778 1955 582909844 582908652 0.000000e+00 1491
24 TraesCS3B01G541600 chr3D 88.991 1199 105 8 778 1955 582920991 582919799 0.000000e+00 1458
25 TraesCS3B01G541600 chr3D 89.562 1073 88 6 796 1850 582922246 582921180 0.000000e+00 1339
26 TraesCS3B01G541600 chr3D 83.361 1214 151 40 781 1975 582992021 582990840 0.000000e+00 1075
27 TraesCS3B01G541600 chr3D 89.134 589 60 3 1 585 583005318 583004730 0.000000e+00 730
28 TraesCS3B01G541600 chr3D 84.000 325 21 13 2585 2904 583000002 582999704 1.700000e-72 283
29 TraesCS3B01G541600 chrUn 85.783 415 46 4 1894 2297 341036616 341037028 7.440000e-116 427
30 TraesCS3B01G541600 chrUn 85.577 416 44 7 1894 2297 41606288 41605877 3.460000e-114 422
31 TraesCS3B01G541600 chrUn 85.577 416 44 7 1894 2297 349985954 349985543 3.460000e-114 422
32 TraesCS3B01G541600 chrUn 85.577 416 44 7 1894 2297 388576797 388576386 3.460000e-114 422
33 TraesCS3B01G541600 chrUn 82.729 469 55 8 586 1032 41611259 41610795 7.540000e-106 394
34 TraesCS3B01G541600 chrUn 82.561 367 29 17 2545 2904 370989039 370988701 1.020000e-74 291
35 TraesCS3B01G541600 chrUn 91.053 190 12 3 2587 2771 41609688 41609499 4.800000e-63 252
36 TraesCS3B01G541600 chrUn 90.355 197 12 5 2582 2771 341037079 341037275 4.800000e-63 252
37 TraesCS3B01G541600 chr2D 79.298 285 42 14 122 397 540148821 540149097 1.780000e-42 183
38 TraesCS3B01G541600 chr2D 77.778 234 40 12 147 373 256714391 256714163 1.820000e-27 134
39 TraesCS3B01G541600 chr2B 78.495 279 40 18 131 395 492610734 492610462 6.440000e-37 165
40 TraesCS3B01G541600 chr3A 78.431 255 40 14 147 390 129558885 129558635 5.010000e-33 152
41 TraesCS3B01G541600 chr5D 76.838 272 51 9 133 395 538995227 538995495 3.020000e-30 143
42 TraesCS3B01G541600 chr4A 76.604 265 54 7 114 373 173755170 173754909 3.900000e-29 139
43 TraesCS3B01G541600 chr6D 86.719 128 11 6 273 395 398723196 398723070 1.400000e-28 137
44 TraesCS3B01G541600 chr5B 86.066 122 11 6 278 394 94716911 94716791 3.040000e-25 126


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 TraesCS3B01G541600 chr3B 779644149 779647052 2903 True 2456.5 4242 100.000000 1 2904 2 chr3B.!!$R11 2903
1 TraesCS3B01G541600 chr3B 779692793 779694533 1740 True 2001.0 2001 87.735000 582 2297 1 chr3B.!!$R2 1715
2 TraesCS3B01G541600 chr3B 780059708 780061451 1743 True 1949.0 1949 87.172000 582 2297 1 chr3B.!!$R8 1715
3 TraesCS3B01G541600 chr3B 780088724 780090468 1744 True 1943.0 1943 87.130000 582 2297 1 chr3B.!!$R9 1715
4 TraesCS3B01G541600 chr3B 779712558 779714542 1984 True 1095.0 1951 88.402000 586 2771 2 chr3B.!!$R12 2185
5 TraesCS3B01G541600 chr3B 779988013 779989590 1577 True 883.0 1520 88.980500 974 2771 2 chr3B.!!$R14 1797
6 TraesCS3B01G541600 chr3B 779974316 779975000 684 True 778.0 778 87.391000 1619 2297 1 chr3B.!!$R6 678
7 TraesCS3B01G541600 chr3B 779997323 779997883 560 True 555.0 555 84.602000 9 581 1 chr3B.!!$R7 572
8 TraesCS3B01G541600 chr3B 780125393 780125951 558 True 553.0 553 84.602000 9 581 1 chr3B.!!$R10 572
9 TraesCS3B01G541600 chr3B 779941230 779941790 560 True 521.0 521 83.592000 9 581 1 chr3B.!!$R4 572
10 TraesCS3B01G541600 chr3B 779812613 779819768 7155 True 348.4 433 87.191000 586 2771 5 chr3B.!!$R13 2185
11 TraesCS3B01G541600 chr3D 582898291 582899808 1517 True 1531.0 1531 85.152000 778 2297 1 chr3D.!!$R1 1519
12 TraesCS3B01G541600 chr3D 582908652 582909844 1192 True 1491.0 1491 89.491000 778 1955 1 chr3D.!!$R2 1177
13 TraesCS3B01G541600 chr3D 582919799 582922246 2447 True 1398.5 1458 89.276500 778 1955 2 chr3D.!!$R4 1177
14 TraesCS3B01G541600 chr3D 582990840 582992021 1181 True 1075.0 1075 83.361000 781 1975 1 chr3D.!!$R3 1194
15 TraesCS3B01G541600 chr3D 582999704 583005318 5614 True 938.0 1801 87.052333 1 2904 3 chr3D.!!$R5 2903
16 TraesCS3B01G541600 chrUn 41605877 41611259 5382 True 356.0 422 86.453000 586 2771 3 chrUn.!!$R4 2185
17 TraesCS3B01G541600 chrUn 341036616 341037275 659 False 339.5 427 88.069000 1894 2771 2 chrUn.!!$F1 877

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
551 573 0.396435 TTGTGTGTCCGAGCATTCCT 59.604 50.0 0.0 0.0 0.00 3.36 F
1224 8059 0.532862 CCAACGCTGTCCTTGAGTGT 60.533 55.0 0.0 0.0 35.67 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1536 12099 1.464734 ACTCAAAGATCTCCTCGCGA 58.535 50.0 9.26 9.26 0.00 5.87 R
2771 14290 0.740737 GCACTGTGGAACTTTGTGCT 59.259 50.0 10.21 0.00 46.72 4.40 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
47 48 2.289820 CCATGATCACGGAATTGCTCTG 59.710 50.000 0.14 0.00 36.38 3.35
49 50 3.885724 TGATCACGGAATTGCTCTGTA 57.114 42.857 0.00 0.00 42.10 2.74
77 78 1.071699 GTGGGAGTGTGCCAAGACTTA 59.928 52.381 0.00 0.00 40.43 2.24
92 93 4.429854 AGACTTAGGAGGCAATTGATCC 57.570 45.455 17.97 17.97 31.22 3.36
118 119 4.039245 TCCACGTCAAAGTTGAAGATCTCT 59.961 41.667 12.92 0.00 38.67 3.10
119 120 4.151335 CCACGTCAAAGTTGAAGATCTCTG 59.849 45.833 12.92 1.93 38.67 3.35
126 127 5.680594 AAGTTGAAGATCTCTGAGCTCAT 57.319 39.130 18.63 1.08 0.00 2.90
232 233 6.148645 GGAGACCACTTCTTCTTTTCTTGATC 59.851 42.308 0.00 0.00 33.22 2.92
251 252 1.480954 TCGAGAACCTATGCCTTGGAC 59.519 52.381 0.00 0.00 0.00 4.02
295 298 2.109834 TCACCACCCATCACCAAAGAAT 59.890 45.455 0.00 0.00 0.00 2.40
318 321 5.001232 TGAAACTTGAGTACTTGGGTATGC 58.999 41.667 0.00 0.00 0.00 3.14
320 323 2.829720 ACTTGAGTACTTGGGTATGCGA 59.170 45.455 0.00 0.00 0.00 5.10
355 375 2.036256 CCAAGCTTGGGGGAGGTG 59.964 66.667 34.08 9.02 44.70 4.00
356 376 2.677875 CAAGCTTGGGGGAGGTGC 60.678 66.667 19.14 0.00 0.00 5.01
357 377 3.984732 AAGCTTGGGGGAGGTGCC 61.985 66.667 0.00 0.00 0.00 5.01
370 390 4.538746 GGAGGTGCCCTAGTATTGTATC 57.461 50.000 0.00 0.00 31.76 2.24
371 391 3.901844 GGAGGTGCCCTAGTATTGTATCA 59.098 47.826 0.00 0.00 31.76 2.15
372 392 4.262506 GGAGGTGCCCTAGTATTGTATCAC 60.263 50.000 0.00 0.00 31.76 3.06
426 446 9.109393 CATGGCATAGTAAAAGTTGTAGTATGT 57.891 33.333 21.44 6.69 37.26 2.29
458 478 5.534278 TGCAATGTGTTCTATTGTTCCTTCA 59.466 36.000 0.00 0.00 37.73 3.02
472 493 6.627395 TGTTCCTTCATGTTTCGTTGTATT 57.373 33.333 0.00 0.00 0.00 1.89
478 499 5.660629 TCATGTTTCGTTGTATTCGTTGT 57.339 34.783 0.00 0.00 0.00 3.32
520 541 7.516198 AAGAATAGCATGAGTGTCTTGTTTT 57.484 32.000 0.00 0.00 0.00 2.43
531 552 8.742554 TGAGTGTCTTGTTTTCTTTTTCTTTC 57.257 30.769 0.00 0.00 0.00 2.62
538 560 8.977505 TCTTGTTTTCTTTTTCTTTCTTGTGTG 58.022 29.630 0.00 0.00 0.00 3.82
542 564 5.229921 TCTTTTTCTTTCTTGTGTGTCCG 57.770 39.130 0.00 0.00 0.00 4.79
549 571 1.795768 TCTTGTGTGTCCGAGCATTC 58.204 50.000 0.00 0.00 0.00 2.67
551 573 0.396435 TTGTGTGTCCGAGCATTCCT 59.604 50.000 0.00 0.00 0.00 3.36
561 583 5.652014 TGTCCGAGCATTCCTATTCAATTTT 59.348 36.000 0.00 0.00 0.00 1.82
616 3628 4.592778 ACCGGTACCAAGAAAAAGGTAGTA 59.407 41.667 4.49 0.00 40.83 1.82
648 3660 1.260561 GGATATACAAGTGTTGCGCCG 59.739 52.381 4.18 0.00 0.00 6.46
649 3661 0.655733 ATATACAAGTGTTGCGCCGC 59.344 50.000 4.18 0.00 0.00 6.53
650 3662 1.688422 TATACAAGTGTTGCGCCGCG 61.688 55.000 8.83 8.83 0.00 6.46
740 3756 3.237268 AGGATGTAAAACCAGCCAACA 57.763 42.857 0.00 0.00 43.42 3.33
743 3759 4.592778 AGGATGTAAAACCAGCCAACAAAT 59.407 37.500 0.00 0.00 43.42 2.32
747 3763 5.734720 TGTAAAACCAGCCAACAAATGAAA 58.265 33.333 0.00 0.00 0.00 2.69
768 3784 9.900090 ATGAAAAGCATCTACGTGTACACGCTA 62.900 40.741 40.21 29.40 45.75 4.26
786 3802 3.778718 CGCTACCGTTTGAAATTGATTCG 59.221 43.478 0.00 0.00 41.18 3.34
825 3844 2.678471 CCCATTTTTGGCACCTCATC 57.322 50.000 0.00 0.00 0.00 2.92
833 3852 2.380064 TGGCACCTCATCAAACCTTT 57.620 45.000 0.00 0.00 0.00 3.11
836 3855 1.546029 GCACCTCATCAAACCTTTCCC 59.454 52.381 0.00 0.00 0.00 3.97
886 3915 5.580691 CGAACAGGAGCAACTACAAATATCA 59.419 40.000 0.00 0.00 0.00 2.15
887 3916 6.455646 CGAACAGGAGCAACTACAAATATCAC 60.456 42.308 0.00 0.00 0.00 3.06
906 3935 2.111043 CCATTCCCCATCGACCCG 59.889 66.667 0.00 0.00 0.00 5.28
910 3939 1.054406 ATTCCCCATCGACCCGTCAT 61.054 55.000 0.00 0.00 0.00 3.06
953 3982 1.582389 AGCTTCTCTTCTCAGGCCAT 58.418 50.000 5.01 0.00 0.00 4.40
974 4003 0.755079 CATCCATCGCCTCTTCTCCA 59.245 55.000 0.00 0.00 0.00 3.86
977 4006 1.208052 TCCATCGCCTCTTCTCCAAAG 59.792 52.381 0.00 0.00 0.00 2.77
978 4007 1.208052 CCATCGCCTCTTCTCCAAAGA 59.792 52.381 0.00 0.00 0.00 2.52
991 4034 5.699097 TCTCCAAAGAAACCAAATAACCG 57.301 39.130 0.00 0.00 0.00 4.44
1005 4048 2.830186 TAACCGGAGCAACCATGGCC 62.830 60.000 13.04 3.10 38.90 5.36
1105 5044 4.020617 CGGAGCAGGCCCAGAACA 62.021 66.667 0.00 0.00 0.00 3.18
1173 7888 2.000701 CCACCTCCCAGCCATGGTA 61.001 63.158 14.67 0.00 46.10 3.25
1218 8053 2.032681 GAGGCCAACGCTGTCCTT 59.967 61.111 5.01 0.00 34.44 3.36
1224 8059 0.532862 CCAACGCTGTCCTTGAGTGT 60.533 55.000 0.00 0.00 35.67 3.55
1305 8700 2.265739 GGTGTCTGCATCGAGCCA 59.734 61.111 0.00 0.00 44.83 4.75
1564 12127 5.584913 AGGAGATCTTTGAGTACTTCAGGA 58.415 41.667 0.00 0.00 37.07 3.86
1632 12226 9.060347 AGTTTATTTATGCACATGGATCTACTG 57.940 33.333 0.00 0.00 0.00 2.74
1650 12613 3.142174 ACTGAGATCTGCATGCATGATG 58.858 45.455 30.64 19.94 34.84 3.07
1799 12842 1.478510 TCTTCAAGACAGAGGCGATCC 59.521 52.381 0.00 0.00 0.00 3.36
1840 12883 2.297701 GAGAGGCTCGTCAAGATCTCT 58.702 52.381 9.22 0.00 40.00 3.10
1897 13371 3.376078 AGGCCAACCAATGCTGCG 61.376 61.111 5.01 0.00 39.06 5.18
1991 13477 7.553334 TCTAGCAATCGATTTGTAAGTTACCT 58.447 34.615 8.21 0.00 37.65 3.08
2054 13555 6.921914 AGGATTGCTTGAGATTTGAAGAAAG 58.078 36.000 0.00 0.00 0.00 2.62
2105 13611 7.585210 GGTACTAAAGAAACAATTTGACGACAC 59.415 37.037 2.79 0.00 0.00 3.67
2107 13613 3.602390 AGAAACAATTTGACGACACCG 57.398 42.857 2.79 0.00 42.50 4.94
2135 13641 4.755266 AGTTTGGTATACTTCGCATCCT 57.245 40.909 2.25 0.00 0.00 3.24
2172 13678 4.201763 GGCGCAAAAATGTTCTTTGTTTCA 60.202 37.500 10.83 0.00 36.38 2.69
2273 13787 3.081409 GCCCCCTGCTCCGTTCTA 61.081 66.667 0.00 0.00 36.87 2.10
2568 14082 9.261035 TCTCAACTTCACTTTAATCCTCTATCT 57.739 33.333 0.00 0.00 0.00 1.98
2569 14083 9.311916 CTCAACTTCACTTTAATCCTCTATCTG 57.688 37.037 0.00 0.00 0.00 2.90
2570 14084 8.816894 TCAACTTCACTTTAATCCTCTATCTGT 58.183 33.333 0.00 0.00 0.00 3.41
2603 14117 6.834168 ATTATTTCTTTCCTTTTCTCGGCA 57.166 33.333 0.00 0.00 0.00 5.69
2638 14157 1.355971 CACGTACCATTTCCACTCCG 58.644 55.000 0.00 0.00 0.00 4.63
2692 14211 0.685131 TCCATTGCTGGCATGGAAGG 60.685 55.000 17.63 1.19 42.80 3.46
2771 14290 6.373216 CGGAAGTTGTAGGTTTTGATTCCATA 59.627 38.462 0.00 0.00 35.72 2.74
2772 14291 7.414098 CGGAAGTTGTAGGTTTTGATTCCATAG 60.414 40.741 0.00 0.00 35.72 2.23
2773 14292 6.759497 AGTTGTAGGTTTTGATTCCATAGC 57.241 37.500 0.00 0.00 0.00 2.97
2774 14293 6.245408 AGTTGTAGGTTTTGATTCCATAGCA 58.755 36.000 0.00 0.00 0.00 3.49
2775 14294 6.151144 AGTTGTAGGTTTTGATTCCATAGCAC 59.849 38.462 0.00 0.00 0.00 4.40
2776 14295 5.565509 TGTAGGTTTTGATTCCATAGCACA 58.434 37.500 0.00 0.00 0.00 4.57
2777 14296 6.007076 TGTAGGTTTTGATTCCATAGCACAA 58.993 36.000 0.00 0.00 0.00 3.33
2778 14297 6.491745 TGTAGGTTTTGATTCCATAGCACAAA 59.508 34.615 0.00 0.00 0.00 2.83
2779 14298 6.029346 AGGTTTTGATTCCATAGCACAAAG 57.971 37.500 0.00 0.00 33.23 2.77
2780 14299 5.539955 AGGTTTTGATTCCATAGCACAAAGT 59.460 36.000 0.00 0.00 33.23 2.66
2781 14300 6.041979 AGGTTTTGATTCCATAGCACAAAGTT 59.958 34.615 0.00 0.00 33.23 2.66
2782 14301 6.366061 GGTTTTGATTCCATAGCACAAAGTTC 59.634 38.462 0.00 0.00 33.23 3.01
2783 14302 5.643379 TTGATTCCATAGCACAAAGTTCC 57.357 39.130 0.00 0.00 0.00 3.62
2784 14303 4.661222 TGATTCCATAGCACAAAGTTCCA 58.339 39.130 0.00 0.00 0.00 3.53
2785 14304 4.458989 TGATTCCATAGCACAAAGTTCCAC 59.541 41.667 0.00 0.00 0.00 4.02
2801 14320 6.156748 AGTTCCACAGTGCATATATACGAA 57.843 37.500 0.00 0.00 0.00 3.85
2802 14321 6.578944 AGTTCCACAGTGCATATATACGAAA 58.421 36.000 0.00 0.00 0.00 3.46
2803 14322 6.479001 AGTTCCACAGTGCATATATACGAAAC 59.521 38.462 0.00 0.00 0.00 2.78
2804 14323 5.294356 TCCACAGTGCATATATACGAAACC 58.706 41.667 0.00 0.00 0.00 3.27
2805 14324 5.053811 CCACAGTGCATATATACGAAACCA 58.946 41.667 0.00 0.00 0.00 3.67
2807 14326 5.522097 CACAGTGCATATATACGAAACCACA 59.478 40.000 0.00 0.00 0.00 4.17
2809 14328 6.423905 ACAGTGCATATATACGAAACCACATC 59.576 38.462 0.00 0.00 0.00 3.06
2810 14329 5.932303 AGTGCATATATACGAAACCACATCC 59.068 40.000 0.00 0.00 0.00 3.51
2811 14330 5.699001 GTGCATATATACGAAACCACATCCA 59.301 40.000 0.00 0.00 0.00 3.41
2813 14332 7.547722 GTGCATATATACGAAACCACATCCATA 59.452 37.037 0.00 0.00 0.00 2.74
2814 14333 7.763985 TGCATATATACGAAACCACATCCATAG 59.236 37.037 0.00 0.00 0.00 2.23
2815 14334 7.764443 GCATATATACGAAACCACATCCATAGT 59.236 37.037 0.00 0.00 0.00 2.12
2816 14335 9.087424 CATATATACGAAACCACATCCATAGTG 57.913 37.037 0.00 0.00 36.76 2.74
2817 14336 2.356135 ACGAAACCACATCCATAGTGC 58.644 47.619 0.00 0.00 35.69 4.40
2818 14337 2.290008 ACGAAACCACATCCATAGTGCA 60.290 45.455 0.00 0.00 35.69 4.57
2819 14338 2.095853 CGAAACCACATCCATAGTGCAC 59.904 50.000 9.40 9.40 35.69 4.57
2820 14339 3.347216 GAAACCACATCCATAGTGCACT 58.653 45.455 25.12 25.12 35.69 4.40
2821 14340 2.698855 ACCACATCCATAGTGCACTC 57.301 50.000 25.56 0.00 35.69 3.51
2822 14341 1.210478 ACCACATCCATAGTGCACTCC 59.790 52.381 25.56 0.00 35.69 3.85
2823 14342 1.210234 CCACATCCATAGTGCACTCCA 59.790 52.381 25.56 7.32 35.69 3.86
2824 14343 2.158711 CCACATCCATAGTGCACTCCAT 60.159 50.000 25.56 9.79 35.69 3.41
2825 14344 3.548770 CACATCCATAGTGCACTCCATT 58.451 45.455 25.56 0.74 0.00 3.16
2826 14345 4.444733 CCACATCCATAGTGCACTCCATTA 60.445 45.833 25.56 5.51 35.69 1.90
2827 14346 4.512944 CACATCCATAGTGCACTCCATTAC 59.487 45.833 25.56 0.00 0.00 1.89
2828 14347 4.164030 ACATCCATAGTGCACTCCATTACA 59.836 41.667 25.56 3.73 0.00 2.41
2829 14348 5.163163 ACATCCATAGTGCACTCCATTACAT 60.163 40.000 25.56 6.40 0.00 2.29
2830 14349 4.960938 TCCATAGTGCACTCCATTACATC 58.039 43.478 25.56 0.00 0.00 3.06
2871 14390 3.118038 TCAAGCCACATAAGGACATACCC 60.118 47.826 0.00 0.00 40.05 3.69
2883 14402 2.378038 GACATACCCCACATGCATTGT 58.622 47.619 0.00 0.00 39.91 2.71
2893 14412 5.593909 CCCCACATGCATTGTCTTATTTCTA 59.406 40.000 0.00 0.00 36.00 2.10
2894 14413 6.460123 CCCCACATGCATTGTCTTATTTCTAC 60.460 42.308 0.00 0.00 36.00 2.59
2897 14416 7.148188 CCACATGCATTGTCTTATTTCTACACT 60.148 37.037 0.00 0.00 36.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 4.042809 TGGTGTGGTTTGAATCTAGTCCAT 59.957 41.667 0.00 0.00 0.00 3.41
16 17 2.150390 CGTGATCATGGTGTGGTTTGA 58.850 47.619 7.06 0.00 0.00 2.69
47 48 2.548480 GCACACTCCCACTTCTGTTTAC 59.452 50.000 0.00 0.00 0.00 2.01
49 50 1.680338 GCACACTCCCACTTCTGTTT 58.320 50.000 0.00 0.00 0.00 2.83
64 65 0.324943 GCCTCCTAAGTCTTGGCACA 59.675 55.000 6.76 0.00 42.79 4.57
77 78 0.849417 GAGGGGATCAATTGCCTCCT 59.151 55.000 16.07 16.07 35.78 3.69
92 93 1.873591 CTTCAACTTTGACGTGGAGGG 59.126 52.381 0.00 0.00 36.83 4.30
168 169 3.258872 CAGCCAAACCCATCATCTTGAAA 59.741 43.478 0.00 0.00 0.00 2.69
232 233 1.802880 CGTCCAAGGCATAGGTTCTCG 60.803 57.143 0.00 0.00 0.00 4.04
251 252 2.480419 GGAACACACTTGTCATCCTTCG 59.520 50.000 3.64 0.00 33.55 3.79
295 298 5.001232 GCATACCCAAGTACTCAAGTTTCA 58.999 41.667 0.00 0.00 0.00 2.69
353 373 4.101119 AGGTGTGATACAATACTAGGGCAC 59.899 45.833 0.00 0.00 0.00 5.01
354 374 4.295201 AGGTGTGATACAATACTAGGGCA 58.705 43.478 0.00 0.00 0.00 5.36
355 375 4.957684 AGGTGTGATACAATACTAGGGC 57.042 45.455 0.00 0.00 0.00 5.19
356 376 8.647796 TGATAAAGGTGTGATACAATACTAGGG 58.352 37.037 0.00 0.00 0.00 3.53
444 464 6.485313 ACAACGAAACATGAAGGAACAATAGA 59.515 34.615 0.00 0.00 0.00 1.98
458 478 6.018588 TCTCAACAACGAATACAACGAAACAT 60.019 34.615 0.00 0.00 34.70 2.71
511 532 8.978539 ACACAAGAAAGAAAAAGAAAACAAGAC 58.021 29.630 0.00 0.00 0.00 3.01
520 541 4.938832 TCGGACACACAAGAAAGAAAAAGA 59.061 37.500 0.00 0.00 0.00 2.52
531 552 0.798776 GGAATGCTCGGACACACAAG 59.201 55.000 0.00 0.00 0.00 3.16
538 560 5.757850 AAATTGAATAGGAATGCTCGGAC 57.242 39.130 0.00 0.00 0.00 4.79
648 3660 2.595386 CTTAACAACTTTGGATGCCGC 58.405 47.619 0.00 0.00 0.00 6.53
649 3661 2.030363 TGCTTAACAACTTTGGATGCCG 60.030 45.455 0.00 0.00 0.00 5.69
650 3662 3.658757 TGCTTAACAACTTTGGATGCC 57.341 42.857 0.00 0.00 0.00 4.40
740 3756 6.599437 GTGTACACGTAGATGCTTTTCATTT 58.401 36.000 10.84 0.00 35.05 2.32
768 3784 6.500041 TCTTTTCGAATCAATTTCAAACGGT 58.500 32.000 0.00 0.00 33.66 4.83
769 3785 6.398935 GCTCTTTTCGAATCAATTTCAAACGG 60.399 38.462 0.00 0.00 33.66 4.44
799 3818 4.812814 CCAAAAATGGGCTAGCGC 57.187 55.556 23.93 23.93 0.00 5.92
825 3844 2.332654 CGGCCGAGGGAAAGGTTTG 61.333 63.158 24.07 0.00 0.00 2.93
861 3884 3.462483 TTTGTAGTTGCTCCTGTTCGA 57.538 42.857 0.00 0.00 0.00 3.71
862 3885 5.580691 TGATATTTGTAGTTGCTCCTGTTCG 59.419 40.000 0.00 0.00 0.00 3.95
874 3897 5.431731 TGGGGAATGGAGTGATATTTGTAGT 59.568 40.000 0.00 0.00 0.00 2.73
886 3915 1.345715 GGGTCGATGGGGAATGGAGT 61.346 60.000 0.00 0.00 0.00 3.85
887 3916 1.451936 GGGTCGATGGGGAATGGAG 59.548 63.158 0.00 0.00 0.00 3.86
906 3935 1.045911 AGGAGCGAGGAAGGGATGAC 61.046 60.000 0.00 0.00 0.00 3.06
910 3939 1.076632 GAGAGGAGCGAGGAAGGGA 60.077 63.158 0.00 0.00 0.00 4.20
953 3982 1.043816 GAGAAGAGGCGATGGATGGA 58.956 55.000 0.00 0.00 0.00 3.41
974 4003 3.892588 TGCTCCGGTTATTTGGTTTCTTT 59.107 39.130 0.00 0.00 0.00 2.52
977 4006 3.571571 GTTGCTCCGGTTATTTGGTTTC 58.428 45.455 0.00 0.00 0.00 2.78
978 4007 2.297880 GGTTGCTCCGGTTATTTGGTTT 59.702 45.455 0.00 0.00 0.00 3.27
1052 4095 0.103572 TAAGAACCGCTCGTATGCCC 59.896 55.000 0.00 0.00 0.00 5.36
1140 5079 0.180406 GGTGGTGTATGGCGGAGATT 59.820 55.000 0.00 0.00 0.00 2.40
1224 8059 3.706373 GGCTCCTGGTGGCGAAGA 61.706 66.667 6.56 0.00 0.00 2.87
1500 12063 4.338879 CCTTGGAGAAGGTGATGAACATT 58.661 43.478 0.00 0.00 43.63 2.71
1536 12099 1.464734 ACTCAAAGATCTCCTCGCGA 58.535 50.000 9.26 9.26 0.00 5.87
1650 12613 3.887110 TGATCCAGTTCCAATCATCATGC 59.113 43.478 0.00 0.00 0.00 4.06
1840 12883 3.142951 CCAAACCTCACGTTGTCCAATA 58.857 45.455 0.00 0.00 33.93 1.90
1897 13371 1.959282 GATGGAATTGTGGATCAGGCC 59.041 52.381 0.00 0.00 0.00 5.19
1964 13450 8.827677 GGTAACTTACAAATCGATTGCTAGATT 58.172 33.333 12.25 5.87 43.13 2.40
2009 13495 4.221482 CCTTTCTTCCCCTGAATTTCAAGG 59.779 45.833 7.02 7.02 0.00 3.61
2010 13496 5.079643 TCCTTTCTTCCCCTGAATTTCAAG 58.920 41.667 0.01 0.00 0.00 3.02
2019 13513 2.494870 CAAGCAATCCTTTCTTCCCCTG 59.505 50.000 0.00 0.00 0.00 4.45
2076 13577 8.339714 TCGTCAAATTGTTTCTTTAGTACCAAG 58.660 33.333 0.00 0.00 0.00 3.61
2105 13611 4.889832 AGTATACCAAACTAGACGACGG 57.110 45.455 0.00 0.00 0.00 4.79
2107 13613 4.732442 GCGAAGTATACCAAACTAGACGAC 59.268 45.833 0.00 0.00 0.00 4.34
2116 13622 4.202223 GGAGAGGATGCGAAGTATACCAAA 60.202 45.833 0.00 0.00 32.21 3.28
2182 13688 5.493133 TTTGTTTGGTCTCACATGTGTAC 57.507 39.130 24.63 21.59 0.00 2.90
2265 13777 6.183360 TGCTCATCTCCAAATAATAGAACGGA 60.183 38.462 0.00 0.00 0.00 4.69
2273 13787 6.252599 TGTAGGTGCTCATCTCCAAATAAT 57.747 37.500 0.00 0.00 0.00 1.28
2543 14057 9.311916 CAGATAGAGGATTAAAGTGAAGTTGAG 57.688 37.037 0.00 0.00 0.00 3.02
2575 14089 9.174166 CCGAGAAAAGGAAAGAAATAATAGGAA 57.826 33.333 0.00 0.00 0.00 3.36
2576 14090 7.282450 GCCGAGAAAAGGAAAGAAATAATAGGA 59.718 37.037 0.00 0.00 0.00 2.94
2577 14091 7.067008 TGCCGAGAAAAGGAAAGAAATAATAGG 59.933 37.037 0.00 0.00 0.00 2.57
2578 14092 7.910683 GTGCCGAGAAAAGGAAAGAAATAATAG 59.089 37.037 0.00 0.00 0.00 1.73
2579 14093 7.413657 CGTGCCGAGAAAAGGAAAGAAATAATA 60.414 37.037 0.00 0.00 0.00 0.98
2580 14094 6.621613 GTGCCGAGAAAAGGAAAGAAATAAT 58.378 36.000 0.00 0.00 0.00 1.28
2581 14095 5.334569 CGTGCCGAGAAAAGGAAAGAAATAA 60.335 40.000 0.00 0.00 0.00 1.40
2582 14096 4.153475 CGTGCCGAGAAAAGGAAAGAAATA 59.847 41.667 0.00 0.00 0.00 1.40
2583 14097 3.058224 CGTGCCGAGAAAAGGAAAGAAAT 60.058 43.478 0.00 0.00 0.00 2.17
2638 14157 4.414337 AATTAGGCATGTCTCTCTCCAC 57.586 45.455 1.25 0.00 0.00 4.02
2692 14211 7.029563 GGATATTCAAACAATGTCAGTGGTTC 58.970 38.462 0.00 0.00 0.00 3.62
2771 14290 0.740737 GCACTGTGGAACTTTGTGCT 59.259 50.000 10.21 0.00 46.72 4.40
2772 14291 3.256620 GCACTGTGGAACTTTGTGC 57.743 52.632 10.21 0.00 45.42 4.57
2773 14292 4.771590 ATATGCACTGTGGAACTTTGTG 57.228 40.909 5.98 0.00 38.04 3.33
2774 14293 6.257849 CGTATATATGCACTGTGGAACTTTGT 59.742 38.462 5.98 0.00 38.04 2.83
2775 14294 6.478673 TCGTATATATGCACTGTGGAACTTTG 59.521 38.462 5.98 0.00 38.04 2.77
2776 14295 6.578944 TCGTATATATGCACTGTGGAACTTT 58.421 36.000 5.98 0.00 38.04 2.66
2777 14296 6.156748 TCGTATATATGCACTGTGGAACTT 57.843 37.500 5.98 0.00 38.04 2.66
2778 14297 5.784578 TCGTATATATGCACTGTGGAACT 57.215 39.130 5.98 0.00 38.04 3.01
2779 14298 6.292703 GGTTTCGTATATATGCACTGTGGAAC 60.293 42.308 5.98 0.00 37.35 3.62
2780 14299 5.756347 GGTTTCGTATATATGCACTGTGGAA 59.244 40.000 5.98 0.00 0.00 3.53
2781 14300 5.163395 TGGTTTCGTATATATGCACTGTGGA 60.163 40.000 10.21 7.28 0.00 4.02
2782 14301 5.050363 GTGGTTTCGTATATATGCACTGTGG 60.050 44.000 10.21 0.00 0.00 4.17
2783 14302 5.522097 TGTGGTTTCGTATATATGCACTGTG 59.478 40.000 2.76 2.76 0.00 3.66
2784 14303 5.666462 TGTGGTTTCGTATATATGCACTGT 58.334 37.500 1.60 0.00 0.00 3.55
2785 14304 6.128553 GGATGTGGTTTCGTATATATGCACTG 60.129 42.308 1.60 0.00 0.00 3.66
2801 14320 2.356125 GGAGTGCACTATGGATGTGGTT 60.356 50.000 21.73 0.00 36.08 3.67
2802 14321 1.210478 GGAGTGCACTATGGATGTGGT 59.790 52.381 21.73 0.00 36.08 4.16
2803 14322 1.210234 TGGAGTGCACTATGGATGTGG 59.790 52.381 21.73 0.00 36.08 4.17
2804 14323 2.696989 TGGAGTGCACTATGGATGTG 57.303 50.000 21.73 0.00 38.36 3.21
2805 14324 3.939740 AATGGAGTGCACTATGGATGT 57.060 42.857 21.73 0.00 0.00 3.06
2807 14326 5.309020 AGATGTAATGGAGTGCACTATGGAT 59.691 40.000 21.73 8.06 0.00 3.41
2809 14328 4.965814 AGATGTAATGGAGTGCACTATGG 58.034 43.478 21.73 0.00 0.00 2.74
2810 14329 8.613060 AATAAGATGTAATGGAGTGCACTATG 57.387 34.615 21.73 0.00 0.00 2.23
2811 14330 9.632638 AAAATAAGATGTAATGGAGTGCACTAT 57.367 29.630 21.73 7.96 0.00 2.12
2813 14332 7.944729 AAAATAAGATGTAATGGAGTGCACT 57.055 32.000 21.88 21.88 0.00 4.40
2814 14333 8.243426 TCAAAAATAAGATGTAATGGAGTGCAC 58.757 33.333 9.40 9.40 0.00 4.57
2815 14334 8.243426 GTCAAAAATAAGATGTAATGGAGTGCA 58.757 33.333 0.00 0.00 0.00 4.57
2816 14335 8.462016 AGTCAAAAATAAGATGTAATGGAGTGC 58.538 33.333 0.00 0.00 0.00 4.40
2825 14344 9.967451 TGACCCAATAGTCAAAAATAAGATGTA 57.033 29.630 0.00 0.00 43.65 2.29
2826 14345 8.877864 TGACCCAATAGTCAAAAATAAGATGT 57.122 30.769 0.00 0.00 43.65 3.06
2843 14362 2.311542 TCCTTATGTGGCTTGACCCAAT 59.688 45.455 0.00 0.00 36.46 3.16
2871 14390 6.968904 GTGTAGAAATAAGACAATGCATGTGG 59.031 38.462 0.00 0.00 44.12 4.17


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

AutoCloner maintained by Alex Coulton.