Multiple sequence alignment - TraesCS1A01G293700

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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 TraesCS1A01G293700 chr1A 100.000 3338 0 0 1 3338 489166556 489163219 0.000000e+00 6165.0
1 TraesCS1A01G293700 chr1A 93.658 473 17 5 2432 2902 24356271 24356732 0.000000e+00 695.0
2 TraesCS1A01G293700 chr1A 93.658 473 17 5 2432 2902 24380722 24381183 0.000000e+00 695.0
3 TraesCS1A01G293700 chr1A 93.003 343 21 3 413 754 164462622 164462282 6.430000e-137 497.0
4 TraesCS1A01G293700 chr1A 86.134 476 19 5 1 430 164462937 164462463 1.400000e-128 470.0
5 TraesCS1A01G293700 chr1A 90.987 233 19 2 227 457 489166187 489165955 2.500000e-81 313.0
6 TraesCS1A01G293700 chr1A 90.987 233 19 2 370 602 489166330 489166100 2.500000e-81 313.0
7 TraesCS1A01G293700 chr1A 76.415 212 21 14 209 392 164462655 164462445 1.650000e-13 87.9
8 TraesCS1A01G293700 chr7A 98.361 915 14 1 2422 3336 56101969 56102882 0.000000e+00 1605.0
9 TraesCS1A01G293700 chr7A 82.812 192 18 7 561 751 11056403 11056580 1.240000e-34 158.0
10 TraesCS1A01G293700 chr6A 98.674 905 11 1 2432 3336 587883381 587882478 0.000000e+00 1604.0
11 TraesCS1A01G293700 chr4D 96.476 908 22 3 2429 3336 399431821 399430924 0.000000e+00 1491.0
12 TraesCS1A01G293700 chr4D 86.341 205 24 4 522 724 297378573 297378371 1.560000e-53 220.0
13 TraesCS1A01G293700 chr5B 96.133 905 24 3 2432 3336 594224484 594223591 0.000000e+00 1467.0
14 TraesCS1A01G293700 chr1D 92.262 1021 49 9 1396 2397 396332567 396333576 0.000000e+00 1421.0
15 TraesCS1A01G293700 chr1D 88.761 694 41 16 749 1408 396331845 396332535 0.000000e+00 815.0
16 TraesCS1A01G293700 chr1D 100.000 35 0 0 2398 2432 396333596 396333630 7.730000e-07 65.8
17 TraesCS1A01G293700 chr6B 97.421 504 12 1 2432 2935 711728130 711728632 0.000000e+00 857.0
18 TraesCS1A01G293700 chr6B 100.000 360 0 0 2977 3336 711728633 711728992 0.000000e+00 665.0
19 TraesCS1A01G293700 chr2A 83.279 921 94 29 2424 3336 716477355 716476487 0.000000e+00 793.0
20 TraesCS1A01G293700 chr2A 82.838 909 99 28 2431 3333 735406817 735407674 0.000000e+00 761.0
21 TraesCS1A01G293700 chr2A 87.084 511 44 11 2827 3333 759033947 759034439 2.910000e-155 558.0
22 TraesCS1A01G293700 chr2B 83.370 914 91 35 2432 3336 9120174 9119313 0.000000e+00 789.0
23 TraesCS1A01G293700 chr1B 86.741 626 44 20 796 1388 523215997 523215378 0.000000e+00 660.0
24 TraesCS1A01G293700 chr1B 82.581 620 85 15 1755 2372 523214950 523214352 2.950000e-145 525.0
25 TraesCS1A01G293700 chr1B 90.390 385 26 6 1988 2372 523240160 523239787 2.310000e-136 496.0
26 TraesCS1A01G293700 chr1B 90.449 356 25 7 1978 2333 523245556 523245210 8.440000e-126 460.0
27 TraesCS1A01G293700 chr1B 80.606 330 60 4 1399 1726 523215335 523215008 5.530000e-63 252.0
28 TraesCS1A01G293700 chr1B 83.032 277 25 8 749 1024 523245854 523245599 7.200000e-57 231.0
29 TraesCS1A01G293700 chr4A 92.899 338 23 1 413 749 148411152 148410815 1.080000e-134 490.0
30 TraesCS1A01G293700 chr4A 83.403 476 33 7 1 430 148411467 148410992 1.870000e-107 399.0
31 TraesCS1A01G293700 chr4A 91.000 100 9 0 127 226 705171737 705171638 5.810000e-28 135.0
32 TraesCS1A01G293700 chr6D 82.544 338 29 9 1 314 60392374 60392043 1.530000e-68 270.0
33 TraesCS1A01G293700 chr6D 86.256 211 23 5 523 731 60392118 60391912 1.210000e-54 224.0
34 TraesCS1A01G293700 chr7D 77.686 484 67 26 1 457 620312320 620312789 1.190000e-64 257.0
35 TraesCS1A01G293700 chr7D 81.515 330 42 15 413 731 620312599 620312920 1.540000e-63 254.0
36 TraesCS1A01G293700 chr7D 88.824 170 17 2 146 314 620312621 620312789 1.210000e-49 207.0
37 TraesCS1A01G293700 chr5D 85.957 235 26 5 492 724 446046724 446046953 9.250000e-61 244.0
38 TraesCS1A01G293700 chr5D 80.139 287 41 11 100 375 446046522 446046803 2.030000e-47 200.0
39 TraesCS1A01G293700 chr5D 84.112 107 15 2 209 314 446046724 446046829 5.890000e-18 102.0
40 TraesCS1A01G293700 chr3D 86.243 189 23 3 127 314 495660736 495660550 5.650000e-48 202.0
41 TraesCS1A01G293700 chr3D 92.623 122 7 2 1 121 313215653 313215773 1.230000e-39 174.0
42 TraesCS1A01G293700 chr3D 82.927 205 20 7 546 749 313216066 313216256 1.590000e-38 171.0
43 TraesCS1A01G293700 chr3D 89.109 101 11 0 648 748 604863397 604863297 3.500000e-25 126.0
44 TraesCS1A01G293700 chr2D 92.683 123 7 2 1 122 427309429 427309550 3.420000e-40 176.0
45 TraesCS1A01G293700 chrUn 88.608 79 7 2 237 314 101231637 101231560 9.860000e-16 95.3
46 TraesCS1A01G293700 chrUn 95.918 49 2 0 270 318 101231635 101231587 2.760000e-11 80.5


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 TraesCS1A01G293700 chr1A 489163219 489166556 3337 True 2263.666667 6165 93.991333 1 3338 3 chr1A.!!$R2 3337
1 TraesCS1A01G293700 chr1A 164462282 164462937 655 True 351.633333 497 85.184000 1 754 3 chr1A.!!$R1 753
2 TraesCS1A01G293700 chr7A 56101969 56102882 913 False 1605.000000 1605 98.361000 2422 3336 1 chr7A.!!$F2 914
3 TraesCS1A01G293700 chr6A 587882478 587883381 903 True 1604.000000 1604 98.674000 2432 3336 1 chr6A.!!$R1 904
4 TraesCS1A01G293700 chr4D 399430924 399431821 897 True 1491.000000 1491 96.476000 2429 3336 1 chr4D.!!$R2 907
5 TraesCS1A01G293700 chr5B 594223591 594224484 893 True 1467.000000 1467 96.133000 2432 3336 1 chr5B.!!$R1 904
6 TraesCS1A01G293700 chr1D 396331845 396333630 1785 False 767.266667 1421 93.674333 749 2432 3 chr1D.!!$F1 1683
7 TraesCS1A01G293700 chr6B 711728130 711728992 862 False 761.000000 857 98.710500 2432 3336 2 chr6B.!!$F1 904
8 TraesCS1A01G293700 chr2A 716476487 716477355 868 True 793.000000 793 83.279000 2424 3336 1 chr2A.!!$R1 912
9 TraesCS1A01G293700 chr2A 735406817 735407674 857 False 761.000000 761 82.838000 2431 3333 1 chr2A.!!$F1 902
10 TraesCS1A01G293700 chr2B 9119313 9120174 861 True 789.000000 789 83.370000 2432 3336 1 chr2B.!!$R1 904
11 TraesCS1A01G293700 chr1B 523214352 523215997 1645 True 479.000000 660 83.309333 796 2372 3 chr1B.!!$R2 1576
12 TraesCS1A01G293700 chr1B 523245210 523245854 644 True 345.500000 460 86.740500 749 2333 2 chr1B.!!$R3 1584
13 TraesCS1A01G293700 chr4A 148410815 148411467 652 True 444.500000 490 88.151000 1 749 2 chr4A.!!$R2 748
14 TraesCS1A01G293700 chr7D 620312320 620312920 600 False 239.333333 257 82.675000 1 731 3 chr7D.!!$F1 730

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
425 504 0.039256 TGAAGTTGCAATGAAGCGCC 60.039 50.0 2.29 0.0 37.31 6.53 F
1048 1150 0.096976 CGCCAACAACACATCGATCC 59.903 55.0 0.00 0.0 0.00 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2221 2417 0.392461 TGTGCTTAACCATCCGGAGC 60.392 55.0 11.34 6.46 35.59 4.70 R
2867 3099 0.179078 ACCACGTCGCAAACCACTTA 60.179 50.0 0.00 0.00 0.00 2.24 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 1.441729 GGCGGTAGCTGCTGTCATA 59.558 57.895 13.43 0.00 44.37 2.15
209 272 2.407428 GGGGCCGTTGAAGCTTAGC 61.407 63.158 0.00 0.00 0.00 3.09
230 293 3.425713 CGCTGCAATGGAGCACGT 61.426 61.111 25.49 0.00 40.11 4.49
281 344 1.512734 CGGAGTTGCAATGAAGCGC 60.513 57.895 0.59 0.00 37.31 5.92
301 364 4.891727 CGGGGATCGCCGGAGTTG 62.892 72.222 36.33 13.23 33.83 3.16
303 366 4.467084 GGGATCGCCGGAGTTGCA 62.467 66.667 5.05 0.00 33.83 4.08
304 367 2.435938 GGATCGCCGGAGTTGCAA 60.436 61.111 5.05 0.00 0.00 4.08
305 368 2.464459 GGATCGCCGGAGTTGCAAG 61.464 63.158 5.05 0.00 0.00 4.01
306 369 2.436646 ATCGCCGGAGTTGCAAGG 60.437 61.111 5.05 0.00 0.00 3.61
307 370 2.852495 GATCGCCGGAGTTGCAAGGA 62.852 60.000 5.05 0.00 0.00 3.36
308 371 2.463589 ATCGCCGGAGTTGCAAGGAA 62.464 55.000 5.05 0.00 0.00 3.36
309 372 2.680913 CGCCGGAGTTGCAAGGAAG 61.681 63.158 5.05 0.00 0.00 3.46
310 373 2.982744 GCCGGAGTTGCAAGGAAGC 61.983 63.158 5.05 0.00 0.00 3.86
311 374 2.680913 CCGGAGTTGCAAGGAAGCG 61.681 63.158 0.00 0.00 37.31 4.68
312 375 2.563427 GGAGTTGCAAGGAAGCGC 59.437 61.111 0.00 0.00 37.31 5.92
313 376 2.563427 GAGTTGCAAGGAAGCGCC 59.437 61.111 2.29 0.00 37.31 6.53
314 377 3.314388 GAGTTGCAAGGAAGCGCCG 62.314 63.158 2.29 0.00 43.43 6.46
358 421 2.107141 GGAGATCGCCGGAGTTGG 59.893 66.667 5.05 0.00 0.00 3.77
370 449 0.960364 GGAGTTGGAATGAAGCGCCA 60.960 55.000 2.29 0.00 0.00 5.69
371 450 0.169009 GAGTTGGAATGAAGCGCCAC 59.831 55.000 2.29 0.00 0.00 5.01
374 453 4.179579 GGAATGAAGCGCCACGGC 62.180 66.667 2.29 0.00 37.85 5.68
411 490 4.598257 CGCAGGGATCGTTGAAGT 57.402 55.556 0.00 0.00 0.00 3.01
412 491 2.840974 CGCAGGGATCGTTGAAGTT 58.159 52.632 0.00 0.00 0.00 2.66
413 492 0.443869 CGCAGGGATCGTTGAAGTTG 59.556 55.000 0.00 0.00 0.00 3.16
414 493 0.169009 GCAGGGATCGTTGAAGTTGC 59.831 55.000 0.00 0.00 0.00 4.17
415 494 1.522668 CAGGGATCGTTGAAGTTGCA 58.477 50.000 0.00 0.00 0.00 4.08
416 495 1.879380 CAGGGATCGTTGAAGTTGCAA 59.121 47.619 0.00 0.00 0.00 4.08
417 496 2.489329 CAGGGATCGTTGAAGTTGCAAT 59.511 45.455 0.59 0.00 0.00 3.56
418 497 2.489329 AGGGATCGTTGAAGTTGCAATG 59.511 45.455 0.59 0.00 36.38 2.82
419 498 2.487762 GGGATCGTTGAAGTTGCAATGA 59.512 45.455 0.59 0.00 44.99 2.57
420 499 3.057596 GGGATCGTTGAAGTTGCAATGAA 60.058 43.478 0.59 0.00 44.33 2.57
421 500 4.161333 GGATCGTTGAAGTTGCAATGAAG 58.839 43.478 0.59 0.00 44.33 3.02
422 501 2.998772 TCGTTGAAGTTGCAATGAAGC 58.001 42.857 0.59 0.00 39.95 3.86
423 502 1.710249 CGTTGAAGTTGCAATGAAGCG 59.290 47.619 0.59 0.00 37.02 4.68
424 503 1.453148 GTTGAAGTTGCAATGAAGCGC 59.547 47.619 0.59 0.00 37.31 5.92
425 504 0.039256 TGAAGTTGCAATGAAGCGCC 60.039 50.000 2.29 0.00 37.31 6.53
426 505 1.067199 GAAGTTGCAATGAAGCGCCG 61.067 55.000 2.29 0.00 37.31 6.46
427 506 3.174573 GTTGCAATGAAGCGCCGC 61.175 61.111 2.29 0.00 37.31 6.53
428 507 4.757354 TTGCAATGAAGCGCCGCG 62.757 61.111 8.83 8.83 37.31 6.46
447 526 3.430862 GGATCGCCGCAGTTGCAA 61.431 61.111 0.00 0.00 42.21 4.08
448 527 2.099062 GATCGCCGCAGTTGCAAG 59.901 61.111 0.00 0.00 42.21 4.01
449 528 3.386867 GATCGCCGCAGTTGCAAGG 62.387 63.158 0.00 0.00 42.21 3.61
450 529 3.899981 ATCGCCGCAGTTGCAAGGA 62.900 57.895 0.00 0.00 42.21 3.36
451 530 3.659092 CGCCGCAGTTGCAAGGAA 61.659 61.111 0.00 0.00 42.21 3.36
452 531 2.256461 GCCGCAGTTGCAAGGAAG 59.744 61.111 0.00 0.00 42.21 3.46
453 532 2.256461 CCGCAGTTGCAAGGAAGC 59.744 61.111 0.00 0.44 42.21 3.86
454 533 2.127118 CGCAGTTGCAAGGAAGCG 60.127 61.111 16.60 16.60 42.21 4.68
455 534 2.429739 GCAGTTGCAAGGAAGCGC 60.430 61.111 0.00 0.00 41.59 5.92
456 535 2.256461 CAGTTGCAAGGAAGCGCC 59.744 61.111 2.29 0.00 37.31 6.53
457 536 3.357079 AGTTGCAAGGAAGCGCCG 61.357 61.111 2.29 0.00 43.43 6.46
474 553 3.181967 GCGGTCAGCGCTGTAGTG 61.182 66.667 34.70 23.20 35.41 2.74
475 554 2.507102 CGGTCAGCGCTGTAGTGG 60.507 66.667 34.70 17.63 0.00 4.00
476 555 2.970639 GGTCAGCGCTGTAGTGGA 59.029 61.111 34.70 13.84 0.00 4.02
477 556 1.153745 GGTCAGCGCTGTAGTGGAG 60.154 63.158 34.70 9.13 0.00 3.86
478 557 1.807573 GTCAGCGCTGTAGTGGAGC 60.808 63.158 34.70 13.15 0.00 4.70
514 593 1.098050 GAGTTGGAATGAAGCGCCAT 58.902 50.000 2.29 0.00 0.00 4.40
559 638 1.197721 CAGGGATCGTTGAAGTTGCAC 59.802 52.381 0.00 0.00 0.00 4.57
666 746 0.320374 TCGTGGTGTTGTCTGATCCC 59.680 55.000 0.00 0.00 0.00 3.85
696 776 2.413765 GTCAGATCGGACGGCTCC 59.586 66.667 10.29 0.00 0.00 4.70
712 793 1.296727 CTCCGGGGCGACTTAAATTC 58.703 55.000 0.00 0.00 0.00 2.17
768 849 5.444877 CGCCAATGTTCAATGTGCATAAAAG 60.445 40.000 0.00 0.00 0.00 2.27
806 887 6.385649 ACATGAAAAATGTACAACGGTCTT 57.614 33.333 0.00 0.00 0.00 3.01
816 897 5.632959 TGTACAACGGTCTTTTGAAACAAG 58.367 37.500 0.00 0.00 0.00 3.16
823 904 5.644636 ACGGTCTTTTGAAACAAGTAGACAA 59.355 36.000 19.69 0.00 35.02 3.18
920 1006 1.063942 GCCCACTTAGCCCTATTTGGT 60.064 52.381 0.00 0.00 0.00 3.67
931 1017 1.474330 CTATTTGGTCCAGCAACCCC 58.526 55.000 0.00 0.00 38.65 4.95
969 1055 0.319641 GTAGGAATCGCACCGGATCC 60.320 60.000 9.46 0.00 34.18 3.36
982 1071 1.739338 CGGATCCCCCTCTTCAGTCG 61.739 65.000 6.06 0.00 0.00 4.18
1040 1142 2.393764 CCAATTCTTCGCCAACAACAC 58.606 47.619 0.00 0.00 0.00 3.32
1048 1150 0.096976 CGCCAACAACACATCGATCC 59.903 55.000 0.00 0.00 0.00 3.36
1059 1167 2.426406 ATCGATCCTGGCTGCGTGA 61.426 57.895 0.00 0.00 0.00 4.35
1062 1170 1.493950 CGATCCTGGCTGCGTGATTC 61.494 60.000 0.00 0.00 0.00 2.52
1084 1201 3.557595 CAGTGCCGATAGTCCAGAAATTC 59.442 47.826 0.00 0.00 0.00 2.17
1212 1334 6.355397 ACGAGAATCATCATCACAAACATC 57.645 37.500 0.00 0.00 33.17 3.06
1234 1356 3.003378 CCAACGAGTTCCTTGTTCTTTCC 59.997 47.826 0.00 0.00 36.08 3.13
1254 1376 4.883759 TCCTCTGATTATCAGGAAGTCCA 58.116 43.478 20.51 0.42 44.39 4.02
1332 1454 1.298014 CCCCAGACACTTCAGCCTC 59.702 63.158 0.00 0.00 0.00 4.70
1352 1474 1.898574 ACTGCTTGAACCCGGCAAG 60.899 57.895 14.05 14.05 44.22 4.01
1424 1590 2.273449 CCTGCAGGAAGGGCGAAT 59.727 61.111 29.88 0.00 37.39 3.34
1425 1591 2.117156 CCTGCAGGAAGGGCGAATG 61.117 63.158 29.88 0.00 37.39 2.67
1553 1719 3.957535 GGATGCCCAAGATGCGCG 61.958 66.667 0.00 0.00 0.00 6.86
1554 1720 3.957535 GATGCCCAAGATGCGCGG 61.958 66.667 8.83 0.00 0.00 6.46
1563 1729 3.357079 GATGCGCGGGCCCATTAG 61.357 66.667 24.92 10.61 38.85 1.73
1733 1899 2.815647 CGCCTCTCTTTGCCGACC 60.816 66.667 0.00 0.00 0.00 4.79
1738 1916 1.006571 TCTCTTTGCCGACCACGAC 60.007 57.895 0.00 0.00 42.66 4.34
1739 1917 1.300620 CTCTTTGCCGACCACGACA 60.301 57.895 0.00 0.00 42.66 4.35
1816 2012 4.590850 TTCACAGATCTGGATATCCACG 57.409 45.455 26.08 15.95 42.01 4.94
1852 2048 2.414950 CTCGTATGACATCGCGAGC 58.585 57.895 16.66 7.23 43.02 5.03
1931 2127 1.673665 CCTGAGCACAACCTCTGGC 60.674 63.158 2.80 0.00 41.85 4.85
1942 2138 2.037136 CCTCTGGCTTGGCTTCACG 61.037 63.158 0.00 0.00 0.00 4.35
1991 2187 4.724602 TCACTGCCTCGTGCGAGC 62.725 66.667 15.32 11.38 45.60 5.03
2100 2296 1.667830 CCGGTCATGTCTGCGTTGT 60.668 57.895 0.00 0.00 0.00 3.32
2101 2297 1.492873 CGGTCATGTCTGCGTTGTG 59.507 57.895 0.00 0.00 0.00 3.33
2150 2346 1.265095 GCATTGAGGATGTGTATGGCG 59.735 52.381 0.00 0.00 38.07 5.69
2172 2368 2.851195 TGCCCTTGAGAAAACAGAGAC 58.149 47.619 0.00 0.00 0.00 3.36
2221 2417 1.852157 TAAAGGCTGGGTGGGCTCAG 61.852 60.000 0.00 0.00 45.85 3.35
2265 2461 2.431260 GCGTTACGTCTTCGGCCA 60.431 61.111 6.63 0.00 41.85 5.36
2288 2484 1.346395 ACCTTGTCATACCGCTGTGAA 59.654 47.619 0.00 0.00 0.00 3.18
2289 2485 2.027192 ACCTTGTCATACCGCTGTGAAT 60.027 45.455 0.00 0.00 0.00 2.57
2290 2486 2.352651 CCTTGTCATACCGCTGTGAATG 59.647 50.000 0.00 0.00 0.00 2.67
2291 2487 3.261580 CTTGTCATACCGCTGTGAATGA 58.738 45.455 0.00 0.00 0.00 2.57
2293 2489 3.197265 TGTCATACCGCTGTGAATGATG 58.803 45.455 8.69 0.00 31.49 3.07
2294 2490 3.118811 TGTCATACCGCTGTGAATGATGA 60.119 43.478 8.69 0.00 31.49 2.92
2295 2491 4.060900 GTCATACCGCTGTGAATGATGAT 58.939 43.478 8.69 0.00 31.49 2.45
2296 2492 4.060205 TCATACCGCTGTGAATGATGATG 58.940 43.478 0.00 0.00 0.00 3.07
2297 2493 2.696989 ACCGCTGTGAATGATGATGA 57.303 45.000 0.00 0.00 0.00 2.92
2298 2494 3.204306 ACCGCTGTGAATGATGATGAT 57.796 42.857 0.00 0.00 0.00 2.45
2299 2495 3.548770 ACCGCTGTGAATGATGATGATT 58.451 40.909 0.00 0.00 0.00 2.57
2300 2496 3.949754 ACCGCTGTGAATGATGATGATTT 59.050 39.130 0.00 0.00 0.00 2.17
2301 2497 4.201980 ACCGCTGTGAATGATGATGATTTG 60.202 41.667 0.00 0.00 0.00 2.32
2302 2498 4.201980 CCGCTGTGAATGATGATGATTTGT 60.202 41.667 0.00 0.00 0.00 2.83
2303 2499 5.007921 CCGCTGTGAATGATGATGATTTGTA 59.992 40.000 0.00 0.00 0.00 2.41
2304 2500 5.905733 CGCTGTGAATGATGATGATTTGTAC 59.094 40.000 0.00 0.00 0.00 2.90
2327 2526 4.504461 CGTACTTCATCTATGGCAAGTGAC 59.496 45.833 0.00 0.00 30.50 3.67
2372 2571 3.458189 GCTCGCTTGTGTATTGTCCTAT 58.542 45.455 0.00 0.00 0.00 2.57
2390 2589 8.213518 TGTCCTATTTTCTATCTGTCAATTGC 57.786 34.615 0.00 0.00 0.00 3.56
2630 2855 7.566760 TTCGTATGAAACTCAATATGGCATT 57.433 32.000 4.78 0.00 0.00 3.56
2867 3099 0.536006 GCTGCTCTGGTTTGGTGTCT 60.536 55.000 0.00 0.00 0.00 3.41
2937 3169 3.995636 TCTTCCTGGTACCTATCAAGCT 58.004 45.455 14.36 0.00 0.00 3.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
230 293 2.031012 CTTCACTGCAGCACCGGA 59.969 61.111 15.27 0.82 0.00 5.14
287 350 2.435938 TTGCAACTCCGGCGATCC 60.436 61.111 9.30 0.00 0.00 3.36
288 351 2.464459 CCTTGCAACTCCGGCGATC 61.464 63.158 9.30 0.00 0.00 3.69
289 352 2.436646 CCTTGCAACTCCGGCGAT 60.437 61.111 9.30 0.00 0.00 4.58
290 353 3.171828 TTCCTTGCAACTCCGGCGA 62.172 57.895 9.30 0.00 0.00 5.54
291 354 2.668212 TTCCTTGCAACTCCGGCG 60.668 61.111 0.00 0.00 0.00 6.46
292 355 2.982744 GCTTCCTTGCAACTCCGGC 61.983 63.158 0.00 0.00 0.00 6.13
293 356 2.680913 CGCTTCCTTGCAACTCCGG 61.681 63.158 0.00 0.00 0.00 5.14
294 357 2.863153 CGCTTCCTTGCAACTCCG 59.137 61.111 0.00 0.00 0.00 4.63
295 358 2.563427 GCGCTTCCTTGCAACTCC 59.437 61.111 0.00 0.00 0.00 3.85
296 359 2.563427 GGCGCTTCCTTGCAACTC 59.437 61.111 7.64 0.00 0.00 3.01
297 360 3.357079 CGGCGCTTCCTTGCAACT 61.357 61.111 7.64 0.00 0.00 3.16
316 379 4.687215 TCCACTGCAGCGCTGACC 62.687 66.667 40.21 23.71 0.00 4.02
317 380 3.117171 CTCCACTGCAGCGCTGAC 61.117 66.667 40.21 29.09 0.00 3.51
343 406 0.179073 CATTCCAACTCCGGCGATCT 60.179 55.000 9.30 0.00 0.00 2.75
358 421 4.179579 GGCCGTGGCGCTTCATTC 62.180 66.667 7.64 0.00 43.06 2.67
399 478 3.829886 TCATTGCAACTTCAACGATCC 57.170 42.857 0.00 0.00 0.00 3.36
400 479 3.605486 GCTTCATTGCAACTTCAACGATC 59.395 43.478 0.00 0.00 0.00 3.69
401 480 3.568538 GCTTCATTGCAACTTCAACGAT 58.431 40.909 0.00 0.00 0.00 3.73
402 481 2.601979 CGCTTCATTGCAACTTCAACGA 60.602 45.455 0.00 0.00 0.00 3.85
403 482 1.710249 CGCTTCATTGCAACTTCAACG 59.290 47.619 0.00 0.00 0.00 4.10
404 483 1.453148 GCGCTTCATTGCAACTTCAAC 59.547 47.619 0.00 0.00 0.00 3.18
405 484 1.602668 GGCGCTTCATTGCAACTTCAA 60.603 47.619 7.64 0.00 0.00 2.69
406 485 0.039256 GGCGCTTCATTGCAACTTCA 60.039 50.000 7.64 0.00 0.00 3.02
407 486 1.067199 CGGCGCTTCATTGCAACTTC 61.067 55.000 7.64 0.00 0.00 3.01
408 487 1.081242 CGGCGCTTCATTGCAACTT 60.081 52.632 7.64 0.00 0.00 2.66
409 488 2.562912 CGGCGCTTCATTGCAACT 59.437 55.556 7.64 0.00 0.00 3.16
410 489 3.174573 GCGGCGCTTCATTGCAAC 61.175 61.111 26.86 0.00 0.00 4.17
411 490 4.757354 CGCGGCGCTTCATTGCAA 62.757 61.111 30.54 0.00 0.00 4.08
430 509 3.386867 CTTGCAACTGCGGCGATCC 62.387 63.158 12.98 0.00 45.83 3.36
431 510 2.099062 CTTGCAACTGCGGCGATC 59.901 61.111 12.98 0.00 45.83 3.69
432 511 3.434319 CCTTGCAACTGCGGCGAT 61.434 61.111 12.98 0.00 45.83 4.58
433 512 4.617520 TCCTTGCAACTGCGGCGA 62.618 61.111 12.98 0.00 45.83 5.54
434 513 3.599792 CTTCCTTGCAACTGCGGCG 62.600 63.158 0.51 0.51 45.83 6.46
435 514 2.256461 CTTCCTTGCAACTGCGGC 59.744 61.111 0.00 0.00 45.83 6.53
436 515 2.256461 GCTTCCTTGCAACTGCGG 59.744 61.111 0.00 0.00 45.83 5.69
437 516 2.127118 CGCTTCCTTGCAACTGCG 60.127 61.111 13.41 13.41 45.83 5.18
438 517 2.429739 GCGCTTCCTTGCAACTGC 60.430 61.111 0.00 0.00 42.50 4.40
439 518 2.256461 GGCGCTTCCTTGCAACTG 59.744 61.111 7.64 0.00 0.00 3.16
440 519 3.357079 CGGCGCTTCCTTGCAACT 61.357 61.111 7.64 0.00 0.00 3.16
458 537 2.507102 CCACTACAGCGCTGACCG 60.507 66.667 42.03 28.56 40.75 4.79
459 538 1.153745 CTCCACTACAGCGCTGACC 60.154 63.158 42.03 0.00 0.00 4.02
460 539 1.807573 GCTCCACTACAGCGCTGAC 60.808 63.158 42.03 16.54 0.00 3.51
461 540 2.573869 GCTCCACTACAGCGCTGA 59.426 61.111 42.03 24.16 0.00 4.26
484 563 1.956629 TTCCAACTCCGGCGATCTCC 61.957 60.000 9.30 0.00 0.00 3.71
485 564 0.105039 ATTCCAACTCCGGCGATCTC 59.895 55.000 9.30 0.00 0.00 2.75
576 655 0.888736 CCATTGCACCTCCGACAACA 60.889 55.000 0.00 0.00 0.00 3.33
696 776 1.925229 TACGAATTTAAGTCGCCCCG 58.075 50.000 14.66 0.00 42.27 5.73
712 793 4.536364 ATCAGCCGATTGATTTGTTACG 57.464 40.909 0.00 0.00 34.17 3.18
768 849 5.484173 TTTCATGTACATCGGAAGCATTC 57.516 39.130 5.07 0.00 46.67 2.67
863 948 7.204604 TGTCCTATTTTCTTTTCCGTTTTTCC 58.795 34.615 0.00 0.00 0.00 3.13
864 949 8.812147 ATGTCCTATTTTCTTTTCCGTTTTTC 57.188 30.769 0.00 0.00 0.00 2.29
916 1002 2.197324 GTGGGGTTGCTGGACCAA 59.803 61.111 0.00 0.00 41.65 3.67
931 1017 0.179119 CCCTAACGCCTTCTACCGTG 60.179 60.000 0.00 0.00 37.79 4.94
969 1055 0.247736 CAAGGACGACTGAAGAGGGG 59.752 60.000 0.00 0.00 0.00 4.79
998 1087 2.866762 GGAGGAGCGCTGTTTTATACTG 59.133 50.000 18.48 0.00 0.00 2.74
1040 1142 2.107750 ACGCAGCCAGGATCGATG 59.892 61.111 0.54 0.00 0.00 3.84
1048 1150 1.792301 CACTGAATCACGCAGCCAG 59.208 57.895 0.00 0.00 36.86 4.85
1059 1167 2.388735 TCTGGACTATCGGCACTGAAT 58.611 47.619 0.00 0.00 0.00 2.57
1062 1170 2.672961 TTTCTGGACTATCGGCACTG 57.327 50.000 0.00 0.00 0.00 3.66
1084 1201 1.680338 GGGATCCAATTGAACCCGAG 58.320 55.000 15.23 0.00 45.22 4.63
1212 1334 3.003378 GGAAAGAACAAGGAACTCGTTGG 59.997 47.826 14.65 0.48 43.66 3.77
1332 1454 3.365265 GCCGGGTTCAAGCAGTGG 61.365 66.667 2.18 0.00 0.00 4.00
1352 1474 1.384222 CCGGGCTGGGTGAAATAAGC 61.384 60.000 3.77 0.00 34.86 3.09
1424 1590 1.750206 CATGAAATTCATCCACGCCCA 59.250 47.619 5.36 0.00 34.28 5.36
1425 1591 1.067516 CCATGAAATTCATCCACGCCC 59.932 52.381 5.36 0.00 34.28 6.13
1553 1719 4.581093 GGGGTCGCTAATGGGCCC 62.581 72.222 17.59 17.59 39.71 5.80
1554 1720 3.133365 ATGGGGTCGCTAATGGGCC 62.133 63.158 0.00 0.00 0.00 5.80
1563 1729 2.511600 CAACGGAGATGGGGTCGC 60.512 66.667 0.00 0.00 0.00 5.19
1674 1840 4.493747 AGTCTTCGGCGCGGCTAC 62.494 66.667 30.60 20.95 0.00 3.58
1685 1851 2.633488 GGAATACCAGCACCAGTCTTC 58.367 52.381 0.00 0.00 35.97 2.87
1733 1899 1.740296 GATCCACCCCGTTGTCGTG 60.740 63.158 0.00 0.00 35.01 4.35
1738 1916 1.227556 GGATCGATCCACCCCGTTG 60.228 63.158 34.65 0.00 46.38 4.10
1739 1917 3.227250 GGATCGATCCACCCCGTT 58.773 61.111 34.65 0.00 46.38 4.44
1760 1938 1.083489 TAGGCACCGATTTCAAAGCG 58.917 50.000 0.00 0.00 40.52 4.68
1816 2012 4.830765 TATGTGCCGGCGCCAGAC 62.831 66.667 35.49 21.46 0.00 3.51
1892 2088 4.883300 GTACTCGGCGCGACCTCG 62.883 72.222 12.10 7.84 43.27 4.63
1942 2138 4.521062 AGCTGCAGATCGTCGGGC 62.521 66.667 20.43 0.00 0.00 6.13
1969 2165 2.936912 GCACGAGGCAGTGAGGTCT 61.937 63.158 15.66 0.00 44.43 3.85
2011 2207 2.086426 CATGTCCGTCCACACGTCG 61.086 63.158 0.00 0.00 45.17 5.12
2014 2210 0.598942 TGTTCATGTCCGTCCACACG 60.599 55.000 0.00 0.00 46.29 4.49
2023 2219 1.003580 TCTTCTGGCCTGTTCATGTCC 59.996 52.381 3.32 0.00 0.00 4.02
2027 2223 2.309755 TCCAATCTTCTGGCCTGTTCAT 59.690 45.455 3.32 0.00 36.32 2.57
2100 2296 2.039879 GGGCAGGTAAGAAAGAACCTCA 59.960 50.000 0.00 0.00 44.43 3.86
2101 2297 2.039879 TGGGCAGGTAAGAAAGAACCTC 59.960 50.000 0.00 0.00 44.43 3.85
2150 2346 3.438434 GTCTCTGTTTTCTCAAGGGCATC 59.562 47.826 0.00 0.00 0.00 3.91
2172 2368 0.519077 GCCCTCGAGAACAGCAAAAG 59.481 55.000 15.71 0.00 0.00 2.27
2221 2417 0.392461 TGTGCTTAACCATCCGGAGC 60.392 55.000 11.34 6.46 35.59 4.70
2288 2484 8.893219 ATGAAGTACGTACAAATCATCATCAT 57.107 30.769 26.55 16.26 0.00 2.45
2289 2485 8.197439 AGATGAAGTACGTACAAATCATCATCA 58.803 33.333 37.17 24.21 41.76 3.07
2290 2486 8.581057 AGATGAAGTACGTACAAATCATCATC 57.419 34.615 37.17 31.74 40.95 2.92
2293 2489 8.916654 CCATAGATGAAGTACGTACAAATCATC 58.083 37.037 33.86 33.86 40.00 2.92
2294 2490 7.385205 GCCATAGATGAAGTACGTACAAATCAT 59.615 37.037 27.37 27.37 32.65 2.45
2295 2491 6.700081 GCCATAGATGAAGTACGTACAAATCA 59.300 38.462 26.55 24.24 0.00 2.57
2296 2492 6.700081 TGCCATAGATGAAGTACGTACAAATC 59.300 38.462 26.55 22.40 0.00 2.17
2297 2493 6.578944 TGCCATAGATGAAGTACGTACAAAT 58.421 36.000 26.55 16.24 0.00 2.32
2298 2494 5.968254 TGCCATAGATGAAGTACGTACAAA 58.032 37.500 26.55 12.30 0.00 2.83
2299 2495 5.585820 TGCCATAGATGAAGTACGTACAA 57.414 39.130 26.55 12.65 0.00 2.41
2300 2496 5.126545 ACTTGCCATAGATGAAGTACGTACA 59.873 40.000 26.55 7.65 0.00 2.90
2301 2497 5.459107 CACTTGCCATAGATGAAGTACGTAC 59.541 44.000 18.10 18.10 0.00 3.67
2302 2498 5.358725 TCACTTGCCATAGATGAAGTACGTA 59.641 40.000 0.00 0.00 0.00 3.57
2303 2499 4.159693 TCACTTGCCATAGATGAAGTACGT 59.840 41.667 0.00 0.00 0.00 3.57
2304 2500 4.504461 GTCACTTGCCATAGATGAAGTACG 59.496 45.833 0.00 0.00 0.00 3.67
2327 2526 4.803088 CGCTGGTCTTTGATCTAAGAGAAG 59.197 45.833 18.19 17.70 34.95 2.85
2372 2571 8.077991 CAGAAACAGCAATTGACAGATAGAAAA 58.922 33.333 10.34 0.00 0.00 2.29
2390 2589 3.514645 ACAAAAGCACAAGCAGAAACAG 58.485 40.909 0.00 0.00 45.49 3.16
2630 2855 0.472471 AAAGGAACGAACCTGCTCCA 59.528 50.000 6.00 0.00 40.49 3.86
2867 3099 0.179078 ACCACGTCGCAAACCACTTA 60.179 50.000 0.00 0.00 0.00 2.24
2937 3169 2.957402 AACTTGGAGATGAACCAGCA 57.043 45.000 0.00 0.00 38.70 4.41


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

AutoCloner maintained by Alex Coulton.