Multiple sequence alignment - TraesCS3A01G539400

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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 TraesCS3A01G539400 chr3A 100.000 2975 0 0 1 2975 750547102 750550076 0.000000e+00 5494
1 TraesCS3A01G539400 chr3D 92.108 1774 72 23 394 2131 614268641 614270382 0.000000e+00 2438
2 TraesCS3A01G539400 chr3D 85.733 750 93 9 2132 2871 614270585 614271330 0.000000e+00 780
3 TraesCS3A01G539400 chr3D 85.787 394 34 8 1 391 614268115 614268489 5.980000e-107 398
4 TraesCS3A01G539400 chr3D 85.354 198 27 2 1666 1862 613917659 613917463 1.400000e-48 204
5 TraesCS3A01G539400 chr3D 78.261 207 39 4 1741 1944 614087324 614087121 8.660000e-26 128
6 TraesCS3A01G539400 chr3B 92.279 1075 60 10 394 1459 823592003 823593063 0.000000e+00 1504
7 TraesCS3A01G539400 chr3B 87.937 572 53 4 1573 2128 823593063 823593634 0.000000e+00 660
8 TraesCS3A01G539400 chr3B 91.698 265 22 0 1 265 823590328 823590592 4.680000e-98 368
9 TraesCS3A01G539400 chr3B 92.473 93 7 0 298 390 823590593 823590685 1.860000e-27 134
10 TraesCS3A01G539400 chr7D 77.313 670 123 21 2132 2790 154201905 154202556 4.680000e-98 368
11 TraesCS3A01G539400 chr2D 77.513 587 102 24 2164 2734 563148665 563148093 2.860000e-85 326
12 TraesCS3A01G539400 chr2D 76.884 584 110 17 2128 2701 601981309 601980741 1.040000e-79 307
13 TraesCS3A01G539400 chrUn 78.435 524 81 23 2132 2641 305830960 305830455 2.230000e-81 313
14 TraesCS3A01G539400 chr7A 78.244 524 82 23 2132 2641 735766967 735766462 1.040000e-79 307
15 TraesCS3A01G539400 chr5D 76.539 601 113 19 2177 2766 548259362 548259945 1.340000e-78 303
16 TraesCS3A01G539400 chr1B 76.080 648 115 28 2128 2759 22156989 22156366 4.820000e-78 302
17 TraesCS3A01G539400 chr5A 75.578 606 118 18 2132 2726 625734700 625734114 3.780000e-69 272


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 TraesCS3A01G539400 chr3A 750547102 750550076 2974 False 5494.000000 5494 100.00000 1 2975 1 chr3A.!!$F1 2974
1 TraesCS3A01G539400 chr3D 614268115 614271330 3215 False 1205.333333 2438 87.87600 1 2871 3 chr3D.!!$F1 2870
2 TraesCS3A01G539400 chr3B 823590328 823593634 3306 False 666.500000 1504 91.09675 1 2128 4 chr3B.!!$F1 2127
3 TraesCS3A01G539400 chr7D 154201905 154202556 651 False 368.000000 368 77.31300 2132 2790 1 chr7D.!!$F1 658
4 TraesCS3A01G539400 chr2D 563148093 563148665 572 True 326.000000 326 77.51300 2164 2734 1 chr2D.!!$R1 570
5 TraesCS3A01G539400 chr2D 601980741 601981309 568 True 307.000000 307 76.88400 2128 2701 1 chr2D.!!$R2 573
6 TraesCS3A01G539400 chrUn 305830455 305830960 505 True 313.000000 313 78.43500 2132 2641 1 chrUn.!!$R1 509
7 TraesCS3A01G539400 chr7A 735766462 735766967 505 True 307.000000 307 78.24400 2132 2641 1 chr7A.!!$R1 509
8 TraesCS3A01G539400 chr5D 548259362 548259945 583 False 303.000000 303 76.53900 2177 2766 1 chr5D.!!$F1 589
9 TraesCS3A01G539400 chr1B 22156366 22156989 623 True 302.000000 302 76.08000 2128 2759 1 chr1B.!!$R1 631
10 TraesCS3A01G539400 chr5A 625734114 625734700 586 True 272.000000 272 75.57800 2132 2726 1 chr5A.!!$R1 594

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
151 152 0.037303 CCCTGACAATCACCAGCAGT 59.963 55.0 0.00 0.0 0.00 4.40 F
605 1956 0.096976 CAATACCGCGACAAGCCAAG 59.903 55.0 8.23 0.0 44.76 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1323 2689 0.685458 GGTAGGGGTAGAAGACGGCA 60.685 60.0 0.00 0.0 0.0 5.69 R
2595 4229 0.036952 ACATCGCTTGTAGCTGCTGT 60.037 50.0 13.43 0.0 39.6 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
68 69 2.202932 ACTGCGACATGATCCGGC 60.203 61.111 0.00 0.00 0.00 6.13
146 147 1.351017 GGTTCTCCCTGACAATCACCA 59.649 52.381 0.00 0.00 0.00 4.17
151 152 0.037303 CCCTGACAATCACCAGCAGT 59.963 55.000 0.00 0.00 0.00 4.40
154 155 2.497138 CTGACAATCACCAGCAGTTCA 58.503 47.619 0.00 0.00 0.00 3.18
156 157 2.158769 TGACAATCACCAGCAGTTCAGT 60.159 45.455 0.00 0.00 0.00 3.41
209 210 4.081030 GCTCGTCCGTCGTCGACA 62.081 66.667 24.13 3.70 40.80 4.35
233 240 4.147449 CCTCGCTGCGGTGGATCA 62.147 66.667 23.03 0.00 0.00 2.92
281 288 6.087423 CGTAGAAGAATAGAGCGATTGTGATG 59.913 42.308 0.00 0.00 0.00 3.07
282 289 6.154203 AGAAGAATAGAGCGATTGTGATGA 57.846 37.500 0.00 0.00 0.00 2.92
283 290 6.215121 AGAAGAATAGAGCGATTGTGATGAG 58.785 40.000 0.00 0.00 0.00 2.90
284 291 4.880759 AGAATAGAGCGATTGTGATGAGG 58.119 43.478 0.00 0.00 0.00 3.86
285 292 2.515926 TAGAGCGATTGTGATGAGGC 57.484 50.000 0.00 0.00 0.00 4.70
286 293 0.529337 AGAGCGATTGTGATGAGGCG 60.529 55.000 0.00 0.00 0.00 5.52
287 294 1.493950 GAGCGATTGTGATGAGGCGG 61.494 60.000 0.00 0.00 0.00 6.13
288 295 3.017323 CGATTGTGATGAGGCGGC 58.983 61.111 0.00 0.00 0.00 6.53
289 296 1.522355 CGATTGTGATGAGGCGGCT 60.522 57.895 13.09 13.09 0.00 5.52
290 297 1.769098 CGATTGTGATGAGGCGGCTG 61.769 60.000 19.63 0.00 0.00 4.85
291 298 0.745845 GATTGTGATGAGGCGGCTGT 60.746 55.000 19.63 4.29 0.00 4.40
358 368 2.282745 GCTTTGCAGACCAGGCCT 60.283 61.111 0.00 0.00 0.00 5.19
383 393 0.819582 GCTGTACATTGCAATGGGCT 59.180 50.000 35.85 21.66 45.15 5.19
391 401 4.067192 ACATTGCAATGGGCTTTTTCTTC 58.933 39.130 35.85 0.00 45.15 2.87
394 404 4.354893 TGCAATGGGCTTTTTCTTCATT 57.645 36.364 0.00 0.00 45.15 2.57
395 405 4.317488 TGCAATGGGCTTTTTCTTCATTC 58.683 39.130 0.00 0.00 45.15 2.67
396 406 4.040706 TGCAATGGGCTTTTTCTTCATTCT 59.959 37.500 0.00 0.00 45.15 2.40
398 408 5.173664 CAATGGGCTTTTTCTTCATTCTCC 58.826 41.667 0.00 0.00 0.00 3.71
461 1810 1.002468 GCCATCATGTAATCACGTGGC 60.002 52.381 17.00 2.23 41.29 5.01
464 1813 3.494626 CCATCATGTAATCACGTGGCTAC 59.505 47.826 17.00 16.67 41.29 3.58
605 1956 0.096976 CAATACCGCGACAAGCCAAG 59.903 55.000 8.23 0.00 44.76 3.61
773 2128 3.734231 CCACATAGTAAGCATACCGTTCG 59.266 47.826 0.00 0.00 32.08 3.95
786 2141 2.567985 ACCGTTCGTTGAGATTTTGGT 58.432 42.857 0.00 0.00 0.00 3.67
804 2159 6.995511 TTTGGTAGCAGCGATAAGTAATTT 57.004 33.333 0.00 0.00 0.00 1.82
883 2238 0.106066 TCCTAACGAGGCCCCGAATA 60.106 55.000 15.86 5.17 43.40 1.75
898 2253 4.576463 CCCCGAATAGATCCAAAAGAGTTG 59.424 45.833 0.00 0.00 0.00 3.16
1125 2491 3.753272 CGTCCTGTTCATCTGGTTCATTT 59.247 43.478 0.00 0.00 36.66 2.32
1130 2496 5.009911 CCTGTTCATCTGGTTCATTTGTTCA 59.990 40.000 0.00 0.00 0.00 3.18
1186 2552 2.040178 CTAAACCTACGGGATGCCTCT 58.960 52.381 0.28 0.00 36.25 3.69
1212 2578 0.106769 TGCAGCCTCAGTTTGGAACA 60.107 50.000 0.00 0.00 0.00 3.18
1223 2589 1.869132 GTTTGGAACAGGTACCGTCAC 59.131 52.381 6.18 5.29 42.39 3.67
1248 2614 3.198068 AGATGGTTATGTCATGTGCGAC 58.802 45.455 0.00 0.00 36.40 5.19
1368 2734 0.258774 ACAAGACCAACCAGCAACCT 59.741 50.000 0.00 0.00 0.00 3.50
1450 2816 3.677976 CGCCGAGTAACTAAATGAACCCT 60.678 47.826 0.00 0.00 0.00 4.34
1488 2854 6.072563 GCTATCTAAGTACTCCCTCGGTAAAG 60.073 46.154 0.00 0.00 0.00 1.85
1494 2860 6.951062 AGTACTCCCTCGGTAAAGTAATAC 57.049 41.667 0.00 0.00 0.00 1.89
1497 2863 4.099113 ACTCCCTCGGTAAAGTAATACAGC 59.901 45.833 0.00 0.00 0.00 4.40
1530 2913 8.864069 AGATCACTACTTTATTGATCTGAACG 57.136 34.615 11.57 0.00 46.77 3.95
1534 2917 7.921214 TCACTACTTTATTGATCTGAACGATCC 59.079 37.037 0.00 0.00 46.52 3.36
1607 2991 7.271223 GGTCGTTCATCAATTATCTGTTTTGTG 59.729 37.037 0.00 0.00 0.00 3.33
1630 3015 9.444600 TGTGAAGTAACTAATTACCATTTCTCC 57.555 33.333 0.00 0.00 41.54 3.71
1730 3115 4.514577 CCTCCGGTACCAGCTGCG 62.515 72.222 13.54 6.32 0.00 5.18
1734 3119 1.038681 TCCGGTACCAGCTGCGAATA 61.039 55.000 13.54 0.00 0.00 1.75
1836 3221 3.567797 GCCGCGCTCATCTGGTTC 61.568 66.667 5.56 0.00 0.00 3.62
1906 3291 1.460305 CCCGGGGATGATGAGGACT 60.460 63.158 14.71 0.00 0.00 3.85
1987 3386 3.747388 GCTAGCATAATGGTGCCACCTTA 60.747 47.826 16.23 11.22 46.19 2.69
2139 3740 9.049523 AGTTATGTACTGAATAATGATGCACAG 57.950 33.333 0.00 0.00 35.19 3.66
2146 3747 4.891168 TGAATAATGATGCACAGAGCCAAT 59.109 37.500 0.00 0.00 44.83 3.16
2154 3755 2.094675 GCACAGAGCCAATACCAACAT 58.905 47.619 0.00 0.00 37.23 2.71
2160 3763 6.712095 CACAGAGCCAATACCAACATACATAT 59.288 38.462 0.00 0.00 0.00 1.78
2206 3812 5.919272 AAGTCGTAAAAGACCAAAGCTAC 57.081 39.130 0.00 0.00 41.83 3.58
2229 3837 5.768164 ACGTGTAGGTGAGGAAAAATGAAAT 59.232 36.000 0.00 0.00 0.00 2.17
2288 3898 8.836413 CAAATTGTACCAAACGACCATATCTAT 58.164 33.333 0.00 0.00 0.00 1.98
2298 3908 6.681729 ACGACCATATCTATACCAACCAAT 57.318 37.500 0.00 0.00 0.00 3.16
2334 3946 6.036083 ACATGACGACGATATTCTTCAAAAGG 59.964 38.462 0.00 0.00 28.54 3.11
2402 4019 2.026262 TCCAACCACAAGGCTAGAATCC 60.026 50.000 0.00 0.00 39.06 3.01
2484 4105 0.109179 GCAAAGACATCGCCATTGCA 60.109 50.000 4.10 0.00 44.29 4.08
2499 4123 4.642885 GCCATTGCAAGGTATAACCAACTA 59.357 41.667 10.60 0.00 37.94 2.24
2502 4126 5.765576 TTGCAAGGTATAACCAACTAGGA 57.234 39.130 0.00 0.00 41.95 2.94
2523 4153 1.203313 TCTAGGCTTTCACCCTGGAGT 60.203 52.381 0.00 0.00 35.36 3.85
2562 4196 4.024048 ACGTAGCACCAAAATTGAAGTCAG 60.024 41.667 0.00 0.00 0.00 3.51
2572 4206 7.122055 ACCAAAATTGAAGTCAGTCAAGTGTTA 59.878 33.333 0.00 0.00 40.72 2.41
2584 4218 2.563620 TCAAGTGTTATCGCCACCACTA 59.436 45.455 0.00 0.00 37.18 2.74
2595 4229 1.473257 GCCACCACTATTCTGCGATCA 60.473 52.381 0.00 0.00 0.00 2.92
2678 4313 7.230510 AGTCTTTGTCCATAGTTTGCATAACAA 59.769 33.333 12.28 1.44 36.13 2.83
2684 4319 4.439974 CCATAGTTTGCATAACAACGCCAT 60.440 41.667 12.28 0.00 38.23 4.40
2747 4382 1.545582 CTTTTGGCGACCACCATCATT 59.454 47.619 0.00 0.00 40.13 2.57
2768 4403 1.069935 GGAGCCATAAGAGGTCGCC 59.930 63.158 0.00 0.00 32.48 5.54
2791 4426 1.596934 CACGGTCTGTAGCCACCAT 59.403 57.895 0.00 0.00 32.33 3.55
2793 4428 1.226974 CGGTCTGTAGCCACCATCG 60.227 63.158 0.00 0.00 32.33 3.84
2794 4429 1.663379 CGGTCTGTAGCCACCATCGA 61.663 60.000 0.00 0.00 32.33 3.59
2806 4441 1.825341 CCATCGATGGCTGACTGGA 59.175 57.895 30.53 0.00 41.75 3.86
2822 4457 2.305927 ACTGGACCTAAATCACCACCAG 59.694 50.000 0.00 0.00 45.78 4.00
2827 4462 4.446371 GACCTAAATCACCACCAGATCTG 58.554 47.826 16.24 16.24 0.00 2.90
2831 4466 6.125029 CCTAAATCACCACCAGATCTGAATT 58.875 40.000 24.62 10.10 0.00 2.17
2838 4473 4.536090 ACCACCAGATCTGAATTAGGACAA 59.464 41.667 24.62 0.00 0.00 3.18
2871 4506 0.745845 ACCATGGACGATGCAGAAGC 60.746 55.000 21.47 0.00 42.57 3.86
2872 4507 0.463295 CCATGGACGATGCAGAAGCT 60.463 55.000 5.56 0.00 42.74 3.74
2873 4508 0.656259 CATGGACGATGCAGAAGCTG 59.344 55.000 0.00 0.00 42.74 4.24
2888 4523 4.738998 CTGCGGCCCCCAACATCA 62.739 66.667 0.00 0.00 0.00 3.07
2889 4524 4.738998 TGCGGCCCCCAACATCAG 62.739 66.667 0.00 0.00 0.00 2.90
2891 4526 4.820744 CGGCCCCCAACATCAGGG 62.821 72.222 0.00 0.00 46.36 4.45
2899 4534 2.355010 CCAACATCAGGGGAAGATCC 57.645 55.000 0.00 0.00 35.23 3.36
2900 4535 1.565759 CCAACATCAGGGGAAGATCCA 59.434 52.381 0.00 0.00 38.64 3.41
2901 4536 2.648059 CAACATCAGGGGAAGATCCAC 58.352 52.381 0.00 0.00 41.37 4.02
2909 4544 2.599677 GGGGAAGATCCACTATCGACT 58.400 52.381 0.00 0.00 36.87 4.18
2910 4545 2.559231 GGGGAAGATCCACTATCGACTC 59.441 54.545 0.00 0.00 36.87 3.36
2911 4546 3.223435 GGGAAGATCCACTATCGACTCA 58.777 50.000 0.00 0.00 38.64 3.41
2912 4547 3.004944 GGGAAGATCCACTATCGACTCAC 59.995 52.174 0.00 0.00 38.64 3.51
2913 4548 3.632604 GGAAGATCCACTATCGACTCACA 59.367 47.826 0.00 0.00 39.79 3.58
2914 4549 4.498345 GGAAGATCCACTATCGACTCACAC 60.498 50.000 0.00 0.00 39.79 3.82
2915 4550 2.952978 AGATCCACTATCGACTCACACC 59.047 50.000 0.00 0.00 39.79 4.16
2916 4551 1.092348 TCCACTATCGACTCACACCG 58.908 55.000 0.00 0.00 0.00 4.94
2917 4552 0.809385 CCACTATCGACTCACACCGT 59.191 55.000 0.00 0.00 0.00 4.83
2918 4553 1.201647 CCACTATCGACTCACACCGTT 59.798 52.381 0.00 0.00 0.00 4.44
2919 4554 2.251040 CACTATCGACTCACACCGTTG 58.749 52.381 0.00 0.00 0.00 4.10
2920 4555 1.269166 CTATCGACTCACACCGTTGC 58.731 55.000 0.00 0.00 0.00 4.17
2921 4556 0.885879 TATCGACTCACACCGTTGCT 59.114 50.000 0.00 0.00 0.00 3.91
2922 4557 0.885879 ATCGACTCACACCGTTGCTA 59.114 50.000 0.00 0.00 0.00 3.49
2923 4558 0.039798 TCGACTCACACCGTTGCTAC 60.040 55.000 0.00 0.00 0.00 3.58
2924 4559 1.007336 CGACTCACACCGTTGCTACC 61.007 60.000 0.00 0.00 0.00 3.18
2925 4560 0.032952 GACTCACACCGTTGCTACCA 59.967 55.000 0.00 0.00 0.00 3.25
2926 4561 0.249741 ACTCACACCGTTGCTACCAC 60.250 55.000 0.00 0.00 0.00 4.16
2927 4562 0.033504 CTCACACCGTTGCTACCACT 59.966 55.000 0.00 0.00 0.00 4.00
2928 4563 0.466543 TCACACCGTTGCTACCACTT 59.533 50.000 0.00 0.00 0.00 3.16
2929 4564 0.865769 CACACCGTTGCTACCACTTC 59.134 55.000 0.00 0.00 0.00 3.01
2930 4565 0.466543 ACACCGTTGCTACCACTTCA 59.533 50.000 0.00 0.00 0.00 3.02
2931 4566 0.865769 CACCGTTGCTACCACTTCAC 59.134 55.000 0.00 0.00 0.00 3.18
2932 4567 0.599204 ACCGTTGCTACCACTTCACG 60.599 55.000 0.00 0.00 0.00 4.35
2933 4568 0.319211 CCGTTGCTACCACTTCACGA 60.319 55.000 0.00 0.00 0.00 4.35
2934 4569 1.060713 CGTTGCTACCACTTCACGAG 58.939 55.000 0.00 0.00 0.00 4.18
2935 4570 1.335597 CGTTGCTACCACTTCACGAGA 60.336 52.381 0.00 0.00 0.00 4.04
2936 4571 2.329379 GTTGCTACCACTTCACGAGAG 58.671 52.381 0.00 0.00 0.00 3.20
2937 4572 1.905637 TGCTACCACTTCACGAGAGA 58.094 50.000 0.00 0.00 0.00 3.10
2938 4573 2.235891 TGCTACCACTTCACGAGAGAA 58.764 47.619 0.00 0.00 0.00 2.87
2939 4574 2.626266 TGCTACCACTTCACGAGAGAAA 59.374 45.455 0.00 0.00 0.00 2.52
2940 4575 2.987821 GCTACCACTTCACGAGAGAAAC 59.012 50.000 0.00 0.00 0.00 2.78
2941 4576 2.528041 ACCACTTCACGAGAGAAACC 57.472 50.000 0.00 0.00 0.00 3.27
2942 4577 1.760613 ACCACTTCACGAGAGAAACCA 59.239 47.619 0.00 0.00 0.00 3.67
2943 4578 2.368875 ACCACTTCACGAGAGAAACCAT 59.631 45.455 0.00 0.00 0.00 3.55
2944 4579 2.738846 CCACTTCACGAGAGAAACCATG 59.261 50.000 0.00 0.00 0.00 3.66
2945 4580 2.158449 CACTTCACGAGAGAAACCATGC 59.842 50.000 0.00 0.00 0.00 4.06
2946 4581 2.224281 ACTTCACGAGAGAAACCATGCA 60.224 45.455 0.00 0.00 0.00 3.96
2947 4582 1.795768 TCACGAGAGAAACCATGCAC 58.204 50.000 0.00 0.00 0.00 4.57
2948 4583 0.798776 CACGAGAGAAACCATGCACC 59.201 55.000 0.00 0.00 0.00 5.01
2949 4584 0.396435 ACGAGAGAAACCATGCACCA 59.604 50.000 0.00 0.00 0.00 4.17
2950 4585 1.202758 ACGAGAGAAACCATGCACCAA 60.203 47.619 0.00 0.00 0.00 3.67
2951 4586 1.879380 CGAGAGAAACCATGCACCAAA 59.121 47.619 0.00 0.00 0.00 3.28
2952 4587 2.489329 CGAGAGAAACCATGCACCAAAT 59.511 45.455 0.00 0.00 0.00 2.32
2953 4588 3.057315 CGAGAGAAACCATGCACCAAATT 60.057 43.478 0.00 0.00 0.00 1.82
2954 4589 4.488879 GAGAGAAACCATGCACCAAATTC 58.511 43.478 0.00 0.00 0.00 2.17
2955 4590 3.896888 AGAGAAACCATGCACCAAATTCA 59.103 39.130 0.00 0.00 0.00 2.57
2956 4591 4.529377 AGAGAAACCATGCACCAAATTCAT 59.471 37.500 0.00 0.00 0.00 2.57
2957 4592 5.716228 AGAGAAACCATGCACCAAATTCATA 59.284 36.000 0.00 0.00 0.00 2.15
2958 4593 6.211184 AGAGAAACCATGCACCAAATTCATAA 59.789 34.615 0.00 0.00 0.00 1.90
2959 4594 6.165577 AGAAACCATGCACCAAATTCATAAC 58.834 36.000 0.00 0.00 0.00 1.89
2960 4595 4.470334 ACCATGCACCAAATTCATAACC 57.530 40.909 0.00 0.00 0.00 2.85
2961 4596 3.119173 ACCATGCACCAAATTCATAACCG 60.119 43.478 0.00 0.00 0.00 4.44
2962 4597 3.446799 CATGCACCAAATTCATAACCGG 58.553 45.455 0.00 0.00 0.00 5.28
2963 4598 1.203523 TGCACCAAATTCATAACCGGC 59.796 47.619 0.00 0.00 0.00 6.13
2964 4599 1.470805 GCACCAAATTCATAACCGGCC 60.471 52.381 0.00 0.00 0.00 6.13
2965 4600 1.136110 CACCAAATTCATAACCGGCCC 59.864 52.381 0.00 0.00 0.00 5.80
2966 4601 0.383949 CCAAATTCATAACCGGCCCG 59.616 55.000 0.00 0.00 0.00 6.13
2967 4602 1.384525 CAAATTCATAACCGGCCCGA 58.615 50.000 3.71 0.00 0.00 5.14
2968 4603 1.953686 CAAATTCATAACCGGCCCGAT 59.046 47.619 3.71 0.00 0.00 4.18
2969 4604 2.358322 AATTCATAACCGGCCCGATT 57.642 45.000 3.71 0.00 0.00 3.34
2970 4605 1.604604 ATTCATAACCGGCCCGATTG 58.395 50.000 3.71 0.00 0.00 2.67
2971 4606 0.464735 TTCATAACCGGCCCGATTGG 60.465 55.000 3.71 0.00 37.09 3.16
2972 4607 1.147376 CATAACCGGCCCGATTGGA 59.853 57.895 3.71 0.00 37.49 3.53
2973 4608 0.250727 CATAACCGGCCCGATTGGAT 60.251 55.000 3.71 0.00 37.49 3.41
2974 4609 0.036306 ATAACCGGCCCGATTGGATC 59.964 55.000 3.71 0.00 37.49 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 2.969238 GGCCGGATCATGTCGCAG 60.969 66.667 5.05 0.00 0.00 5.18
143 144 1.620819 CTCCTACACTGAACTGCTGGT 59.379 52.381 0.00 0.00 0.00 4.00
146 147 4.142359 CGAATACTCCTACACTGAACTGCT 60.142 45.833 0.00 0.00 0.00 4.24
151 152 4.851843 TCTCCGAATACTCCTACACTGAA 58.148 43.478 0.00 0.00 0.00 3.02
154 155 5.113446 TCTTCTCCGAATACTCCTACACT 57.887 43.478 0.00 0.00 0.00 3.55
156 157 4.079901 ACCTCTTCTCCGAATACTCCTACA 60.080 45.833 0.00 0.00 0.00 2.74
233 240 1.202463 CGTCTGCCTTCCGATTGATCT 60.202 52.381 0.00 0.00 0.00 2.75
286 293 3.112709 GAAGACGACGCCACAGCC 61.113 66.667 0.00 0.00 34.57 4.85
287 294 3.470567 CGAAGACGACGCCACAGC 61.471 66.667 0.00 0.00 42.66 4.40
288 295 2.254350 TCGAAGACGACGCCACAG 59.746 61.111 0.00 0.00 43.81 3.66
358 368 2.268762 TTGCAATGTACAGCTGTCCA 57.731 45.000 25.56 19.98 0.00 4.02
361 371 1.820519 CCCATTGCAATGTACAGCTGT 59.179 47.619 31.87 25.12 34.60 4.40
405 1754 4.700213 AGTCCCATATGTTTGTGCAGTAAC 59.300 41.667 1.24 0.00 0.00 2.50
583 1934 1.702491 GGCTTGTCGCGGTATTGGAC 61.702 60.000 6.13 0.00 40.44 4.02
605 1956 3.818387 CAGCATCATTCAACCGATATGC 58.182 45.455 0.00 0.00 39.93 3.14
671 2022 2.009774 GATGATGGTGTTCCTCAACCG 58.990 52.381 0.00 0.00 31.75 4.44
739 2090 6.374333 TGCTTACTATGTGGGTTTTGATCTTC 59.626 38.462 0.00 0.00 0.00 2.87
744 2095 5.883673 GGTATGCTTACTATGTGGGTTTTGA 59.116 40.000 9.39 0.00 0.00 2.69
773 2128 2.742053 TCGCTGCTACCAAAATCTCAAC 59.258 45.455 0.00 0.00 0.00 3.18
786 2141 7.307160 GCATGTACAAATTACTTATCGCTGCTA 60.307 37.037 0.00 0.00 0.00 3.49
804 2159 3.135712 ACGGGGAAATCTATGCATGTACA 59.864 43.478 10.16 0.00 0.00 2.90
883 2238 8.325046 AGTAGCTTAATCAACTCTTTTGGATCT 58.675 33.333 0.00 0.00 0.00 2.75
937 2295 2.416747 TGAGAGGATCGTTGCTTTGTG 58.583 47.619 0.00 0.00 42.67 3.33
1125 2491 8.458573 AACCTAATAATCAACACAAGTGAACA 57.541 30.769 7.28 0.00 0.00 3.18
1186 2552 2.938451 CAAACTGAGGCTGCAATCGATA 59.062 45.455 0.00 0.00 0.00 2.92
1223 2589 3.133691 CACATGACATAACCATCTCCGG 58.866 50.000 0.00 0.00 0.00 5.14
1323 2689 0.685458 GGTAGGGGTAGAAGACGGCA 60.685 60.000 0.00 0.00 0.00 5.69
1368 2734 2.125552 CGGCGAGGAACTGATGCA 60.126 61.111 0.00 0.00 41.55 3.96
1372 2738 2.676822 AGCTCGGCGAGGAACTGA 60.677 61.111 35.03 0.00 41.55 3.41
1488 2854 5.970023 AGTGATCTAAACGACGCTGTATTAC 59.030 40.000 0.00 0.00 0.00 1.89
1494 2860 4.017380 AGTAGTGATCTAAACGACGCTG 57.983 45.455 0.00 0.00 0.00 5.18
1497 2863 8.610855 TCAATAAAGTAGTGATCTAAACGACG 57.389 34.615 0.00 0.00 0.00 5.12
1560 2943 8.105197 ACGACCTTAATTAATTACTCCCTTTGT 58.895 33.333 7.43 0.00 0.00 2.83
1563 2946 8.323567 TGAACGACCTTAATTAATTACTCCCTT 58.676 33.333 7.43 0.00 0.00 3.95
1630 3015 9.701098 CAACCTATTTTCATGATTAATCCCATG 57.299 33.333 12.90 11.10 40.97 3.66
1730 3115 1.084289 GGTGCCGTCAGGTTGTATTC 58.916 55.000 0.00 0.00 40.50 1.75
1734 3119 1.600636 CATGGTGCCGTCAGGTTGT 60.601 57.895 0.00 0.00 40.50 3.32
1906 3291 6.258947 TCATGTTTCTTGTTGTTGTCATCGTA 59.741 34.615 0.00 0.00 0.00 3.43
1940 3325 1.273267 TGTGGTCCTCAGAGGCTACAT 60.273 52.381 19.43 0.00 34.61 2.29
1950 3335 1.550327 CTAGCTGACTGTGGTCCTCA 58.450 55.000 0.00 0.00 41.47 3.86
1987 3386 3.524095 TGGTTTTGACTCATGGTGGAT 57.476 42.857 0.00 0.00 0.00 3.41
2091 3490 3.753305 GCAAAGCGCTTTCTAACAAAC 57.247 42.857 31.63 10.45 37.77 2.93
2139 3740 8.615878 TTGTATATGTATGTTGGTATTGGCTC 57.384 34.615 0.00 0.00 0.00 4.70
2171 3777 8.958043 GTCTTTTACGACTTTACTAGTTTTCGA 58.042 33.333 17.02 0.00 37.17 3.71
2175 3781 8.947055 TTGGTCTTTTACGACTTTACTAGTTT 57.053 30.769 0.00 0.00 37.17 2.66
2182 3788 6.144402 CGTAGCTTTGGTCTTTTACGACTTTA 59.856 38.462 0.00 0.00 36.84 1.85
2206 3812 5.682943 TTTCATTTTTCCTCACCTACACG 57.317 39.130 0.00 0.00 0.00 4.49
2229 3837 6.168389 GGATCTAAACACTTCGGGTTTTCTA 58.832 40.000 0.00 0.00 39.12 2.10
2288 3898 5.386060 TGTGGTGTCATAAATTGGTTGGTA 58.614 37.500 0.00 0.00 0.00 3.25
2298 3908 2.990514 CGTCGTCATGTGGTGTCATAAA 59.009 45.455 0.00 0.00 0.00 1.40
2358 3970 1.980951 GATGACGGCAGCGCATGAAA 61.981 55.000 11.47 0.00 0.00 2.69
2437 4055 1.067354 CCTTGTTGAAGGCATTGCTCC 60.067 52.381 8.82 0.00 42.60 4.70
2484 4105 6.497606 GCCTAGATCCTAGTTGGTTATACCTT 59.502 42.308 0.00 0.00 39.58 3.50
2523 4153 2.741092 GTGCACCCGGTCTTGAGA 59.259 61.111 5.22 0.00 0.00 3.27
2550 4184 7.576236 CGATAACACTTGACTGACTTCAATTT 58.424 34.615 0.00 0.00 34.96 1.82
2551 4185 6.347725 GCGATAACACTTGACTGACTTCAATT 60.348 38.462 0.00 0.00 34.96 2.32
2562 4196 1.463444 GTGGTGGCGATAACACTTGAC 59.537 52.381 0.85 0.00 38.83 3.18
2572 4206 0.530650 CGCAGAATAGTGGTGGCGAT 60.531 55.000 0.00 0.00 46.65 4.58
2595 4229 0.036952 ACATCGCTTGTAGCTGCTGT 60.037 50.000 13.43 0.00 39.60 4.40
2678 4313 1.079405 CGGTGGTTGACTATGGCGT 60.079 57.895 0.00 0.00 0.00 5.68
2684 4319 1.191535 CCAGATCCGGTGGTTGACTA 58.808 55.000 0.00 0.00 0.00 2.59
2747 4382 0.824109 CGACCTCTTATGGCTCCACA 59.176 55.000 0.00 0.00 0.00 4.17
2768 4403 1.226603 GGCTACAGACCGTGCTACG 60.227 63.158 2.27 2.27 42.11 3.51
2791 4426 0.033503 TAGGTCCAGTCAGCCATCGA 60.034 55.000 0.00 0.00 0.00 3.59
2793 4428 3.118261 TGATTTAGGTCCAGTCAGCCATC 60.118 47.826 0.00 0.00 0.00 3.51
2794 4429 2.846206 TGATTTAGGTCCAGTCAGCCAT 59.154 45.455 0.00 0.00 0.00 4.40
2799 4434 2.304761 GGTGGTGATTTAGGTCCAGTCA 59.695 50.000 0.00 0.00 0.00 3.41
2806 4441 4.104086 TCAGATCTGGTGGTGATTTAGGT 58.896 43.478 22.42 0.00 0.00 3.08
2822 4457 3.309954 GCGTGGTTGTCCTAATTCAGATC 59.690 47.826 0.00 0.00 34.23 2.75
2827 4462 3.006940 TCATGCGTGGTTGTCCTAATTC 58.993 45.455 5.98 0.00 34.23 2.17
2831 4466 1.470805 CGATCATGCGTGGTTGTCCTA 60.471 52.381 5.98 0.00 34.23 2.94
2838 4473 0.811219 CATGGTCGATCATGCGTGGT 60.811 55.000 24.78 0.00 38.16 4.16
2871 4506 4.738998 TGATGTTGGGGGCCGCAG 62.739 66.667 23.18 0.00 0.00 5.18
2872 4507 4.738998 CTGATGTTGGGGGCCGCA 62.739 66.667 20.63 20.63 0.00 5.69
2874 4509 4.820744 CCCTGATGTTGGGGGCCG 62.821 72.222 0.00 0.00 40.97 6.13
2879 4514 1.133668 GGATCTTCCCCTGATGTTGGG 60.134 57.143 0.00 0.00 44.19 4.12
2880 4515 1.565759 TGGATCTTCCCCTGATGTTGG 59.434 52.381 0.00 0.00 35.03 3.77
2881 4516 2.240667 AGTGGATCTTCCCCTGATGTTG 59.759 50.000 0.00 0.00 35.03 3.33
2882 4517 2.566746 AGTGGATCTTCCCCTGATGTT 58.433 47.619 0.00 0.00 35.03 2.71
2883 4518 2.277008 AGTGGATCTTCCCCTGATGT 57.723 50.000 0.00 0.00 35.03 3.06
2884 4519 3.056250 CGATAGTGGATCTTCCCCTGATG 60.056 52.174 0.00 0.00 35.03 3.07
2885 4520 3.169099 CGATAGTGGATCTTCCCCTGAT 58.831 50.000 0.00 0.00 35.03 2.90
2886 4521 2.177016 TCGATAGTGGATCTTCCCCTGA 59.823 50.000 0.00 0.00 35.03 3.86
2887 4522 2.297597 GTCGATAGTGGATCTTCCCCTG 59.702 54.545 0.00 0.00 35.03 4.45
2888 4523 2.178106 AGTCGATAGTGGATCTTCCCCT 59.822 50.000 0.00 0.00 35.03 4.79
2889 4524 2.559231 GAGTCGATAGTGGATCTTCCCC 59.441 54.545 0.00 0.00 35.03 4.81
2890 4525 3.004944 GTGAGTCGATAGTGGATCTTCCC 59.995 52.174 0.00 0.00 35.03 3.97
2891 4526 3.632604 TGTGAGTCGATAGTGGATCTTCC 59.367 47.826 0.00 0.00 36.96 3.46
2892 4527 4.498345 GGTGTGAGTCGATAGTGGATCTTC 60.498 50.000 0.00 0.00 31.70 2.87
2893 4528 3.381908 GGTGTGAGTCGATAGTGGATCTT 59.618 47.826 0.00 0.00 31.70 2.40
2894 4529 2.952978 GGTGTGAGTCGATAGTGGATCT 59.047 50.000 0.00 0.00 31.70 2.75
2895 4530 2.287069 CGGTGTGAGTCGATAGTGGATC 60.287 54.545 0.00 0.00 37.40 3.36
2896 4531 1.676529 CGGTGTGAGTCGATAGTGGAT 59.323 52.381 0.00 0.00 37.40 3.41
2897 4532 1.092348 CGGTGTGAGTCGATAGTGGA 58.908 55.000 0.00 0.00 37.40 4.02
2898 4533 0.809385 ACGGTGTGAGTCGATAGTGG 59.191 55.000 0.00 0.00 37.40 4.00
2899 4534 2.251040 CAACGGTGTGAGTCGATAGTG 58.749 52.381 0.00 0.00 37.40 2.74
2900 4535 1.402456 GCAACGGTGTGAGTCGATAGT 60.402 52.381 0.66 0.00 37.40 2.12
2901 4536 1.135373 AGCAACGGTGTGAGTCGATAG 60.135 52.381 0.66 0.00 0.00 2.08
2902 4537 0.885879 AGCAACGGTGTGAGTCGATA 59.114 50.000 0.66 0.00 0.00 2.92
2903 4538 0.885879 TAGCAACGGTGTGAGTCGAT 59.114 50.000 0.66 0.00 0.00 3.59
2904 4539 0.039798 GTAGCAACGGTGTGAGTCGA 60.040 55.000 0.66 0.00 0.00 4.20
2905 4540 1.007336 GGTAGCAACGGTGTGAGTCG 61.007 60.000 0.66 0.00 0.00 4.18
2906 4541 0.032952 TGGTAGCAACGGTGTGAGTC 59.967 55.000 0.66 0.00 0.00 3.36
2907 4542 0.249741 GTGGTAGCAACGGTGTGAGT 60.250 55.000 0.66 0.00 0.00 3.41
2908 4543 0.033504 AGTGGTAGCAACGGTGTGAG 59.966 55.000 0.66 0.00 0.00 3.51
2909 4544 0.466543 AAGTGGTAGCAACGGTGTGA 59.533 50.000 0.66 0.00 0.00 3.58
2910 4545 0.865769 GAAGTGGTAGCAACGGTGTG 59.134 55.000 0.66 0.00 0.00 3.82
2911 4546 0.466543 TGAAGTGGTAGCAACGGTGT 59.533 50.000 0.66 0.00 0.00 4.16
2912 4547 0.865769 GTGAAGTGGTAGCAACGGTG 59.134 55.000 0.00 0.00 0.00 4.94
2913 4548 0.599204 CGTGAAGTGGTAGCAACGGT 60.599 55.000 8.60 0.00 0.00 4.83
2914 4549 0.319211 TCGTGAAGTGGTAGCAACGG 60.319 55.000 14.73 0.33 0.00 4.44
2915 4550 1.060713 CTCGTGAAGTGGTAGCAACG 58.939 55.000 9.91 9.91 0.00 4.10
2916 4551 2.030185 TCTCTCGTGAAGTGGTAGCAAC 60.030 50.000 0.00 0.00 0.00 4.17
2917 4552 2.235891 TCTCTCGTGAAGTGGTAGCAA 58.764 47.619 0.00 0.00 0.00 3.91
2918 4553 1.905637 TCTCTCGTGAAGTGGTAGCA 58.094 50.000 0.00 0.00 0.00 3.49
2919 4554 2.987821 GTTTCTCTCGTGAAGTGGTAGC 59.012 50.000 0.00 0.00 0.00 3.58
2920 4555 3.005472 TGGTTTCTCTCGTGAAGTGGTAG 59.995 47.826 0.00 0.00 0.00 3.18
2921 4556 2.960384 TGGTTTCTCTCGTGAAGTGGTA 59.040 45.455 0.00 0.00 0.00 3.25
2922 4557 1.760613 TGGTTTCTCTCGTGAAGTGGT 59.239 47.619 0.00 0.00 0.00 4.16
2923 4558 2.526304 TGGTTTCTCTCGTGAAGTGG 57.474 50.000 0.00 0.00 0.00 4.00
2924 4559 2.158449 GCATGGTTTCTCTCGTGAAGTG 59.842 50.000 0.00 0.00 0.00 3.16
2925 4560 2.224281 TGCATGGTTTCTCTCGTGAAGT 60.224 45.455 0.00 0.00 0.00 3.01
2926 4561 2.158449 GTGCATGGTTTCTCTCGTGAAG 59.842 50.000 0.00 0.00 0.00 3.02
2927 4562 2.143122 GTGCATGGTTTCTCTCGTGAA 58.857 47.619 0.00 0.00 0.00 3.18
2928 4563 1.608025 GGTGCATGGTTTCTCTCGTGA 60.608 52.381 0.00 0.00 0.00 4.35
2929 4564 0.798776 GGTGCATGGTTTCTCTCGTG 59.201 55.000 0.00 0.00 0.00 4.35
2930 4565 0.396435 TGGTGCATGGTTTCTCTCGT 59.604 50.000 0.00 0.00 0.00 4.18
2931 4566 1.522668 TTGGTGCATGGTTTCTCTCG 58.477 50.000 0.00 0.00 0.00 4.04
2932 4567 4.022068 TGAATTTGGTGCATGGTTTCTCTC 60.022 41.667 0.00 0.00 0.00 3.20
2933 4568 3.896888 TGAATTTGGTGCATGGTTTCTCT 59.103 39.130 0.00 0.00 0.00 3.10
2934 4569 4.255833 TGAATTTGGTGCATGGTTTCTC 57.744 40.909 0.00 0.00 0.00 2.87
2935 4570 4.895668 ATGAATTTGGTGCATGGTTTCT 57.104 36.364 0.00 0.00 0.00 2.52
2936 4571 5.351189 GGTTATGAATTTGGTGCATGGTTTC 59.649 40.000 0.00 0.00 0.00 2.78
2937 4572 5.244755 GGTTATGAATTTGGTGCATGGTTT 58.755 37.500 0.00 0.00 0.00 3.27
2938 4573 4.620332 CGGTTATGAATTTGGTGCATGGTT 60.620 41.667 0.00 0.00 0.00 3.67
2939 4574 3.119173 CGGTTATGAATTTGGTGCATGGT 60.119 43.478 0.00 0.00 0.00 3.55
2940 4575 3.446799 CGGTTATGAATTTGGTGCATGG 58.553 45.455 0.00 0.00 0.00 3.66
2941 4576 3.446799 CCGGTTATGAATTTGGTGCATG 58.553 45.455 0.00 0.00 0.00 4.06
2942 4577 2.159114 GCCGGTTATGAATTTGGTGCAT 60.159 45.455 1.90 0.00 0.00 3.96
2943 4578 1.203523 GCCGGTTATGAATTTGGTGCA 59.796 47.619 1.90 0.00 0.00 4.57
2944 4579 1.470805 GGCCGGTTATGAATTTGGTGC 60.471 52.381 1.90 0.00 0.00 5.01
2945 4580 1.136110 GGGCCGGTTATGAATTTGGTG 59.864 52.381 1.90 0.00 0.00 4.17
2946 4581 1.480789 GGGCCGGTTATGAATTTGGT 58.519 50.000 1.90 0.00 0.00 3.67
2947 4582 0.383949 CGGGCCGGTTATGAATTTGG 59.616 55.000 20.56 0.00 0.00 3.28
2948 4583 1.384525 TCGGGCCGGTTATGAATTTG 58.615 50.000 27.98 0.00 0.00 2.32
2949 4584 2.358322 ATCGGGCCGGTTATGAATTT 57.642 45.000 27.98 0.00 0.00 1.82
2950 4585 1.953686 CAATCGGGCCGGTTATGAATT 59.046 47.619 26.11 12.58 0.00 2.17
2951 4586 1.604604 CAATCGGGCCGGTTATGAAT 58.395 50.000 26.11 6.11 0.00 2.57
2952 4587 0.464735 CCAATCGGGCCGGTTATGAA 60.465 55.000 26.11 3.38 0.00 2.57
2953 4588 1.147376 CCAATCGGGCCGGTTATGA 59.853 57.895 26.11 4.28 0.00 2.15
2954 4589 0.250727 ATCCAATCGGGCCGGTTATG 60.251 55.000 26.11 18.52 36.21 1.90
2955 4590 0.036306 GATCCAATCGGGCCGGTTAT 59.964 55.000 26.11 15.95 36.21 1.89
2956 4591 1.448497 GATCCAATCGGGCCGGTTA 59.552 57.895 26.11 10.97 36.21 2.85
2957 4592 2.192175 GATCCAATCGGGCCGGTT 59.808 61.111 27.98 24.51 36.21 4.44


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

AutoCloner maintained by Alex Coulton.