Multiple sequence alignment - TraesCS1D01G372600

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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 TraesCS1D01G372600 chr1D 100.000 3440 0 0 1 3440 450758617 450755178 0.000000e+00 6353.0
1 TraesCS1D01G372600 chr1D 85.829 2357 185 69 594 2877 451036085 451033805 0.000000e+00 2364.0
2 TraesCS1D01G372600 chr1D 82.986 1534 201 33 638 2131 450578841 450580354 0.000000e+00 1332.0
3 TraesCS1D01G372600 chr1D 87.456 1148 119 19 1006 2130 450739243 450740388 0.000000e+00 1299.0
4 TraesCS1D01G372600 chr1D 83.665 1255 161 31 890 2111 451044081 451042838 0.000000e+00 1142.0
5 TraesCS1D01G372600 chr1D 91.287 505 43 1 2933 3437 81452787 81453290 0.000000e+00 688.0
6 TraesCS1D01G372600 chr1D 85.408 233 22 4 3 224 451036721 451036490 7.420000e-57 231.0
7 TraesCS1D01G372600 chr1A 86.604 1799 168 35 594 2349 545764342 545762574 0.000000e+00 1919.0
8 TraesCS1D01G372600 chr1A 84.176 1365 175 27 1007 2347 545752036 545753383 0.000000e+00 1286.0
9 TraesCS1D01G372600 chr1A 82.599 1408 188 29 628 1993 545778680 545777288 0.000000e+00 1190.0
10 TraesCS1D01G372600 chr1A 81.063 602 54 36 2385 2934 545762496 545761903 3.170000e-115 425.0
11 TraesCS1D01G372600 chr1A 76.433 157 17 12 383 520 545859933 545859778 2.220000e-07 67.6
12 TraesCS1D01G372600 chr1B 85.216 1691 162 44 594 2235 618699315 618697664 0.000000e+00 1657.0
13 TraesCS1D01G372600 chr1B 84.604 1312 148 33 720 1993 619095862 619094567 0.000000e+00 1254.0
14 TraesCS1D01G372600 chr1B 82.227 1491 206 38 655 2121 618908384 618906929 0.000000e+00 1230.0
15 TraesCS1D01G372600 chr1B 86.420 1134 126 19 1006 2131 618196983 618198096 0.000000e+00 1216.0
16 TraesCS1D01G372600 chr1B 85.977 1141 142 16 1006 2131 618316850 618317987 0.000000e+00 1205.0
17 TraesCS1D01G372600 chr1B 86.074 517 28 17 2457 2934 618697381 618696870 1.830000e-142 516.0
18 TraesCS1D01G372600 chr1B 90.789 228 19 2 1 227 618699797 618699571 1.550000e-78 303.0
19 TraesCS1D01G372600 chr1B 83.333 180 9 12 224 394 618699539 618699372 2.770000e-31 147.0
20 TraesCS1D01G372600 chr2D 95.303 511 21 3 2931 3440 401551412 401551920 0.000000e+00 808.0
21 TraesCS1D01G372600 chr2D 95.079 508 24 1 2933 3440 390401749 390402255 0.000000e+00 798.0
22 TraesCS1D01G372600 chr2D 92.927 509 33 2 2933 3440 591305472 591305978 0.000000e+00 737.0
23 TraesCS1D01G372600 chr4B 93.023 516 33 3 2926 3440 481630265 481630778 0.000000e+00 750.0
24 TraesCS1D01G372600 chr2A 92.520 508 36 2 2933 3440 717950647 717951152 0.000000e+00 726.0
25 TraesCS1D01G372600 chr5A 91.228 513 37 5 2933 3440 666862484 666862993 0.000000e+00 691.0
26 TraesCS1D01G372600 chr3D 90.962 520 37 5 2930 3440 508431071 508430553 0.000000e+00 691.0
27 TraesCS1D01G372600 chr5D 90.963 509 43 3 2933 3440 305584121 305584627 0.000000e+00 682.0


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 TraesCS1D01G372600 chr1D 450755178 450758617 3439 True 6353.00 6353 100.0000 1 3440 1 chr1D.!!$R1 3439
1 TraesCS1D01G372600 chr1D 450578841 450580354 1513 False 1332.00 1332 82.9860 638 2131 1 chr1D.!!$F2 1493
2 TraesCS1D01G372600 chr1D 450739243 450740388 1145 False 1299.00 1299 87.4560 1006 2130 1 chr1D.!!$F3 1124
3 TraesCS1D01G372600 chr1D 451033805 451036721 2916 True 1297.50 2364 85.6185 3 2877 2 chr1D.!!$R3 2874
4 TraesCS1D01G372600 chr1D 451042838 451044081 1243 True 1142.00 1142 83.6650 890 2111 1 chr1D.!!$R2 1221
5 TraesCS1D01G372600 chr1D 81452787 81453290 503 False 688.00 688 91.2870 2933 3437 1 chr1D.!!$F1 504
6 TraesCS1D01G372600 chr1A 545752036 545753383 1347 False 1286.00 1286 84.1760 1007 2347 1 chr1A.!!$F1 1340
7 TraesCS1D01G372600 chr1A 545777288 545778680 1392 True 1190.00 1190 82.5990 628 1993 1 chr1A.!!$R1 1365
8 TraesCS1D01G372600 chr1A 545761903 545764342 2439 True 1172.00 1919 83.8335 594 2934 2 chr1A.!!$R3 2340
9 TraesCS1D01G372600 chr1B 619094567 619095862 1295 True 1254.00 1254 84.6040 720 1993 1 chr1B.!!$R2 1273
10 TraesCS1D01G372600 chr1B 618906929 618908384 1455 True 1230.00 1230 82.2270 655 2121 1 chr1B.!!$R1 1466
11 TraesCS1D01G372600 chr1B 618196983 618198096 1113 False 1216.00 1216 86.4200 1006 2131 1 chr1B.!!$F1 1125
12 TraesCS1D01G372600 chr1B 618316850 618317987 1137 False 1205.00 1205 85.9770 1006 2131 1 chr1B.!!$F2 1125
13 TraesCS1D01G372600 chr1B 618696870 618699797 2927 True 655.75 1657 86.3530 1 2934 4 chr1B.!!$R3 2933
14 TraesCS1D01G372600 chr2D 401551412 401551920 508 False 808.00 808 95.3030 2931 3440 1 chr2D.!!$F2 509
15 TraesCS1D01G372600 chr2D 390401749 390402255 506 False 798.00 798 95.0790 2933 3440 1 chr2D.!!$F1 507
16 TraesCS1D01G372600 chr2D 591305472 591305978 506 False 737.00 737 92.9270 2933 3440 1 chr2D.!!$F3 507
17 TraesCS1D01G372600 chr4B 481630265 481630778 513 False 750.00 750 93.0230 2926 3440 1 chr4B.!!$F1 514
18 TraesCS1D01G372600 chr2A 717950647 717951152 505 False 726.00 726 92.5200 2933 3440 1 chr2A.!!$F1 507
19 TraesCS1D01G372600 chr5A 666862484 666862993 509 False 691.00 691 91.2280 2933 3440 1 chr5A.!!$F1 507
20 TraesCS1D01G372600 chr3D 508430553 508431071 518 True 691.00 691 90.9620 2930 3440 1 chr3D.!!$R1 510
21 TraesCS1D01G372600 chr5D 305584121 305584627 506 False 682.00 682 90.9630 2933 3440 1 chr5D.!!$F1 507

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
475 533 0.179084 CGCGGACCCATCACAATACT 60.179 55.0 0.00 0.0 0.00 2.12 F
501 559 0.452184 CACACACCTCGTCTCGCTAT 59.548 55.0 0.00 0.0 0.00 2.97 F
711 814 0.459585 GCGCGTTCCCACTCATAGAA 60.460 55.0 8.43 0.0 0.00 2.10 F
2139 2391 0.038892 TCCACGCAGGAGAAACGTAC 60.039 55.0 0.00 0.0 43.07 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2136 2388 0.029567 CGACTGGATCAGCCTCGTAC 59.970 60.0 0.0 0.00 37.63 3.67 R
2139 2391 0.738975 TAACGACTGGATCAGCCTCG 59.261 55.0 0.0 6.44 36.50 4.63 R
2327 2681 0.749454 GTCGCAATGGGGAGCAGAAT 60.749 55.0 0.0 0.00 36.56 2.40 R
3025 3512 1.504359 CGTTTGCGGTTTCTAGTCCA 58.496 50.0 0.0 0.00 0.00 4.02 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
39 40 1.525619 GACACGCGCCAGATATTTACC 59.474 52.381 5.73 0.00 0.00 2.85
108 120 0.744771 GAGCTTTCTTTCCCGGCGAT 60.745 55.000 9.30 0.00 0.00 4.58
209 222 1.975680 TCGGGCTAAAGAGAAACTGGT 59.024 47.619 0.00 0.00 0.00 4.00
217 230 1.645710 AGAGAAACTGGTGTCGGGAT 58.354 50.000 0.00 0.00 0.00 3.85
224 237 2.202756 GGTGTCGGGATGTCGCTC 60.203 66.667 0.00 0.00 0.00 5.03
295 344 2.935955 CACACGAAACAGTCCGGC 59.064 61.111 0.00 0.00 0.00 6.13
313 362 2.032634 CGGCGCCGCACCATATAAT 61.033 57.895 38.48 0.00 0.00 1.28
327 379 7.488150 CGCACCATATAATATACAGTACAGTGG 59.512 40.741 0.42 0.00 0.00 4.00
328 380 7.764443 GCACCATATAATATACAGTACAGTGGG 59.236 40.741 0.42 0.00 0.00 4.61
329 381 8.812972 CACCATATAATATACAGTACAGTGGGT 58.187 37.037 0.42 0.00 0.00 4.51
330 382 8.812972 ACCATATAATATACAGTACAGTGGGTG 58.187 37.037 0.42 0.00 0.00 4.61
331 383 7.764443 CCATATAATATACAGTACAGTGGGTGC 59.236 40.741 0.42 0.00 0.00 5.01
336 388 1.071471 AGTACAGTGGGTGCAGTGC 59.929 57.895 8.58 8.58 34.11 4.40
337 389 1.227823 GTACAGTGGGTGCAGTGCA 60.228 57.895 15.37 15.37 35.60 4.57
362 414 3.443045 GGTGGACTTGGCATGCCG 61.443 66.667 30.87 20.22 39.42 5.69
389 447 0.974383 AAACGACCAACCGAGGAGAT 59.026 50.000 0.00 0.00 0.00 2.75
403 461 0.681243 GGAGATCCCAACTGGCCAAC 60.681 60.000 7.01 0.00 34.14 3.77
405 463 0.329596 AGATCCCAACTGGCCAACTC 59.670 55.000 7.01 0.00 0.00 3.01
407 465 2.484287 ATCCCAACTGGCCAACTCCG 62.484 60.000 7.01 0.00 0.00 4.63
408 466 3.365265 CCAACTGGCCAACTCCGC 61.365 66.667 7.01 0.00 0.00 5.54
409 467 2.281761 CAACTGGCCAACTCCGCT 60.282 61.111 7.01 0.00 0.00 5.52
411 469 3.553095 AACTGGCCAACTCCGCTCC 62.553 63.158 7.01 0.00 0.00 4.70
412 470 4.785453 CTGGCCAACTCCGCTCCC 62.785 72.222 7.01 0.00 0.00 4.30
414 472 4.035102 GGCCAACTCCGCTCCCTT 62.035 66.667 0.00 0.00 0.00 3.95
415 473 2.436824 GCCAACTCCGCTCCCTTC 60.437 66.667 0.00 0.00 0.00 3.46
416 474 3.068881 CCAACTCCGCTCCCTTCA 58.931 61.111 0.00 0.00 0.00 3.02
417 475 1.078848 CCAACTCCGCTCCCTTCAG 60.079 63.158 0.00 0.00 0.00 3.02
418 476 1.078848 CAACTCCGCTCCCTTCAGG 60.079 63.158 0.00 0.00 0.00 3.86
419 477 1.536662 AACTCCGCTCCCTTCAGGT 60.537 57.895 0.00 0.00 36.75 4.00
420 478 1.831652 AACTCCGCTCCCTTCAGGTG 61.832 60.000 0.00 0.00 36.75 4.00
425 483 4.785453 CTCCCTTCAGGTGCGCCC 62.785 72.222 14.07 5.76 36.75 6.13
445 503 1.335132 GCTGACTTCCACCCCCGATA 61.335 60.000 0.00 0.00 0.00 2.92
446 504 1.200519 CTGACTTCCACCCCCGATAA 58.799 55.000 0.00 0.00 0.00 1.75
457 515 2.273557 CCCCCGATAAGTTTACACACG 58.726 52.381 0.00 0.00 0.00 4.49
459 517 1.322338 CCCGATAAGTTTACACACGCG 59.678 52.381 3.53 3.53 0.00 6.01
460 518 1.322338 CCGATAAGTTTACACACGCGG 59.678 52.381 12.47 1.27 0.00 6.46
463 521 1.782044 TAAGTTTACACACGCGGACC 58.218 50.000 12.47 0.00 0.00 4.46
466 524 0.952010 GTTTACACACGCGGACCCAT 60.952 55.000 12.47 0.00 0.00 4.00
467 525 0.671163 TTTACACACGCGGACCCATC 60.671 55.000 12.47 0.00 0.00 3.51
468 526 1.817911 TTACACACGCGGACCCATCA 61.818 55.000 12.47 0.00 0.00 3.07
469 527 2.495366 TACACACGCGGACCCATCAC 62.495 60.000 12.47 0.00 0.00 3.06
470 528 3.621805 ACACGCGGACCCATCACA 61.622 61.111 12.47 0.00 0.00 3.58
471 529 2.358125 CACGCGGACCCATCACAA 60.358 61.111 12.47 0.00 0.00 3.33
472 530 1.745115 CACGCGGACCCATCACAAT 60.745 57.895 12.47 0.00 0.00 2.71
473 531 0.461163 CACGCGGACCCATCACAATA 60.461 55.000 12.47 0.00 0.00 1.90
474 532 0.461339 ACGCGGACCCATCACAATAC 60.461 55.000 12.47 0.00 0.00 1.89
475 533 0.179084 CGCGGACCCATCACAATACT 60.179 55.000 0.00 0.00 0.00 2.12
476 534 1.299541 GCGGACCCATCACAATACTG 58.700 55.000 0.00 0.00 0.00 2.74
477 535 1.406887 GCGGACCCATCACAATACTGT 60.407 52.381 0.00 0.00 35.63 3.55
499 557 1.452953 TTCACACACCTCGTCTCGCT 61.453 55.000 0.00 0.00 0.00 4.93
501 559 0.452184 CACACACCTCGTCTCGCTAT 59.548 55.000 0.00 0.00 0.00 2.97
528 586 5.163982 GCGACCAAGACTTTGACAACTATAC 60.164 44.000 0.00 0.00 36.36 1.47
530 588 5.235516 ACCAAGACTTTGACAACTATACCG 58.764 41.667 0.00 0.00 36.36 4.02
531 589 4.092968 CCAAGACTTTGACAACTATACCGC 59.907 45.833 0.00 0.00 36.36 5.68
532 590 4.803098 AGACTTTGACAACTATACCGCT 57.197 40.909 0.00 0.00 0.00 5.52
533 591 4.745649 AGACTTTGACAACTATACCGCTC 58.254 43.478 0.00 0.00 0.00 5.03
535 593 4.243270 ACTTTGACAACTATACCGCTCAC 58.757 43.478 0.00 0.00 0.00 3.51
536 594 3.945981 TTGACAACTATACCGCTCACA 57.054 42.857 0.00 0.00 0.00 3.58
539 597 4.242475 TGACAACTATACCGCTCACAAAG 58.758 43.478 0.00 0.00 0.00 2.77
543 601 5.351465 ACAACTATACCGCTCACAAAGATTG 59.649 40.000 0.00 0.00 0.00 2.67
558 616 5.774690 ACAAAGATTGCACCTTCCAAGAATA 59.225 36.000 1.47 0.00 0.00 1.75
559 617 6.267471 ACAAAGATTGCACCTTCCAAGAATAA 59.733 34.615 1.47 0.00 0.00 1.40
570 628 2.170397 TCCAAGAATAATCGGCTGAGCA 59.830 45.455 6.82 0.00 0.00 4.26
571 629 2.945008 CCAAGAATAATCGGCTGAGCAA 59.055 45.455 6.82 0.00 0.00 3.91
609 703 8.848182 ACTTTAATGGTTTGACACGGTTTAATA 58.152 29.630 0.00 0.00 0.00 0.98
646 742 1.004277 CGAGATAATCTGACGCGGGC 61.004 60.000 12.47 1.95 0.00 6.13
649 745 1.542030 AGATAATCTGACGCGGGCTAG 59.458 52.381 12.47 2.72 0.00 3.42
710 813 1.141019 GCGCGTTCCCACTCATAGA 59.859 57.895 8.43 0.00 0.00 1.98
711 814 0.459585 GCGCGTTCCCACTCATAGAA 60.460 55.000 8.43 0.00 0.00 2.10
712 815 1.560923 CGCGTTCCCACTCATAGAAG 58.439 55.000 0.00 0.00 0.00 2.85
713 816 1.802880 CGCGTTCCCACTCATAGAAGG 60.803 57.143 0.00 0.00 0.00 3.46
715 818 2.093658 GCGTTCCCACTCATAGAAGGAA 60.094 50.000 0.00 0.00 34.27 3.36
716 819 3.432326 GCGTTCCCACTCATAGAAGGAAT 60.432 47.826 0.00 0.00 38.77 3.01
719 822 3.318313 TCCCACTCATAGAAGGAATCCC 58.682 50.000 0.00 0.00 0.00 3.85
721 824 2.548920 CCACTCATAGAAGGAATCCCGC 60.549 54.545 0.00 0.00 37.58 6.13
763 875 0.690762 TCGAGGGCCTAAACAGCTTT 59.309 50.000 5.73 0.00 0.00 3.51
779 891 1.068588 GCTTTCTTCCCACGCCTTTTT 59.931 47.619 0.00 0.00 0.00 1.94
785 897 1.006220 CCCACGCCTTTTTGCTTCC 60.006 57.895 0.00 0.00 0.00 3.46
792 904 2.094957 CGCCTTTTTGCTTCCGGATTTA 60.095 45.455 4.15 0.00 0.00 1.40
822 956 1.877443 ACACACGCCATGTTCTAAACC 59.123 47.619 0.00 0.00 40.64 3.27
829 963 5.180492 CACGCCATGTTCTAAACCTTTCTTA 59.820 40.000 0.00 0.00 0.00 2.10
831 965 6.433093 ACGCCATGTTCTAAACCTTTCTTATT 59.567 34.615 0.00 0.00 0.00 1.40
833 967 7.148239 CGCCATGTTCTAAACCTTTCTTATTCT 60.148 37.037 0.00 0.00 0.00 2.40
834 968 8.184848 GCCATGTTCTAAACCTTTCTTATTCTC 58.815 37.037 0.00 0.00 0.00 2.87
835 969 8.678199 CCATGTTCTAAACCTTTCTTATTCTCC 58.322 37.037 0.00 0.00 0.00 3.71
836 970 9.231297 CATGTTCTAAACCTTTCTTATTCTCCA 57.769 33.333 0.00 0.00 0.00 3.86
842 976 6.884280 AACCTTTCTTATTCTCCACAAGTG 57.116 37.500 0.00 0.00 0.00 3.16
859 993 2.234143 AGTGCAAAGCCTTCCTTTCTC 58.766 47.619 0.00 0.00 41.75 2.87
958 1111 3.050619 CTCGACAACAGAGTACCAACAC 58.949 50.000 0.00 0.00 0.00 3.32
979 1137 2.092699 CCAACCACAACAACCCCAATTT 60.093 45.455 0.00 0.00 0.00 1.82
1011 1188 2.408271 AGATCAAGATGGCGAGCAAA 57.592 45.000 0.00 0.00 0.00 3.68
1971 2202 2.413765 GAGGGCTGGATCGACGTC 59.586 66.667 5.18 5.18 0.00 4.34
1974 2205 1.826921 GGGCTGGATCGACGTCCTA 60.827 63.158 10.58 0.00 39.12 2.94
2122 2371 1.744741 GAGCACAGCAGCTTCCTCC 60.745 63.158 0.00 0.00 46.75 4.30
2139 2391 0.038892 TCCACGCAGGAGAAACGTAC 60.039 55.000 0.00 0.00 43.07 3.67
2165 2426 2.868583 CTGATCCAGTCGTTAGGCATTG 59.131 50.000 0.00 0.00 0.00 2.82
2184 2445 6.313658 GGCATTGTCAGTTTTTGAAGAGTTTT 59.686 34.615 0.00 0.00 37.61 2.43
2203 2464 3.658757 TTGTTTCTGGCCAATTAGTGC 57.341 42.857 7.01 0.00 0.00 4.40
2217 2481 6.697019 GCCAATTAGTGCCATGTAGTAAATTG 59.303 38.462 10.67 10.67 0.00 2.32
2237 2588 5.478233 TTGTTAGTGCAAACAGTACTGTG 57.522 39.130 28.55 17.93 43.44 3.66
2349 2704 3.195698 GCTCCCCATTGCGACGTC 61.196 66.667 5.18 5.18 0.00 4.34
2373 2766 8.214472 GTCAACGAATTCAAAGAAAAATTAGGC 58.786 33.333 6.22 0.00 0.00 3.93
2374 2767 8.141268 TCAACGAATTCAAAGAAAAATTAGGCT 58.859 29.630 6.22 0.00 0.00 4.58
2375 2768 7.873739 ACGAATTCAAAGAAAAATTAGGCTG 57.126 32.000 6.22 0.00 0.00 4.85
2379 2772 8.593492 AATTCAAAGAAAAATTAGGCTGTGTC 57.407 30.769 0.00 0.00 0.00 3.67
2381 2774 4.766404 AAGAAAAATTAGGCTGTGTCCG 57.234 40.909 0.00 0.00 0.00 4.79
2395 2794 3.923864 TCCGCCGAATCCGATGGG 61.924 66.667 0.00 0.00 38.22 4.00
2489 2916 1.735920 CAGCGTGGACACAGAGCTC 60.736 63.158 5.27 5.27 39.02 4.09
2526 2953 4.713946 GGTGAATCTTCCACCGCA 57.286 55.556 0.00 0.00 43.80 5.69
2571 2998 2.968697 CAGCGTCACTGCACTGCA 60.969 61.111 3.11 3.11 40.19 4.41
2838 3305 2.280524 TTTCGAGTGGGTGTGCCG 60.281 61.111 0.00 0.00 34.97 5.69
2909 3395 0.610687 GAGAACTGGCAGGCTAGTGT 59.389 55.000 20.34 2.05 37.81 3.55
2924 3410 6.533367 CAGGCTAGTGTTTATCTGTTTCTCTC 59.467 42.308 0.00 0.00 0.00 3.20
2925 3411 6.211584 AGGCTAGTGTTTATCTGTTTCTCTCA 59.788 38.462 0.00 0.00 0.00 3.27
3026 3513 2.503809 CCGAAAATTGCGGCGGTG 60.504 61.111 9.78 0.00 42.55 4.94
3344 3848 3.074369 TCGGCCTCCTTCGATGCA 61.074 61.111 0.00 0.00 31.74 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 0.599204 CGGGTAAATATCTGGCGCGT 60.599 55.000 8.43 0.00 0.00 6.01
28 29 6.998802 AGAGAAGATTCCGGGTAAATATCTG 58.001 40.000 0.00 0.00 0.00 2.90
86 98 1.912371 GCCGGGAAAGAAAGCTCGTG 61.912 60.000 2.18 0.00 0.00 4.35
209 222 2.710902 CCTGAGCGACATCCCGACA 61.711 63.158 0.00 0.00 0.00 4.35
217 230 1.134367 CGGAAATACTCCTGAGCGACA 59.866 52.381 0.00 0.00 42.85 4.35
224 237 1.749634 AGACCGACGGAAATACTCCTG 59.250 52.381 23.38 0.00 42.85 3.86
240 288 4.762289 ACATCCATCTAGAACCAAGACC 57.238 45.455 0.00 0.00 0.00 3.85
295 344 0.738063 TATTATATGGTGCGGCGCCG 60.738 55.000 43.13 43.13 36.72 6.46
310 359 5.659525 ACTGCACCCACTGTACTGTATATTA 59.340 40.000 4.96 0.00 0.00 0.98
311 360 4.469945 ACTGCACCCACTGTACTGTATATT 59.530 41.667 4.96 0.00 0.00 1.28
313 362 3.194755 CACTGCACCCACTGTACTGTATA 59.805 47.826 4.96 0.00 0.00 1.47
343 395 2.359850 GCATGCCAAGTCCACCGA 60.360 61.111 6.36 0.00 0.00 4.69
362 414 1.299089 GTTGGTCGTTTGCCACTGC 60.299 57.895 0.00 0.00 35.46 4.40
389 447 2.843545 GGAGTTGGCCAGTTGGGA 59.156 61.111 5.11 0.00 40.01 4.37
403 461 2.581354 CACCTGAAGGGAGCGGAG 59.419 66.667 0.56 0.00 40.27 4.63
408 466 4.785453 GGGCGCACCTGAAGGGAG 62.785 72.222 10.83 0.00 40.27 4.30
423 481 4.410400 GGGGTGGAAGTCAGCGGG 62.410 72.222 0.00 0.00 44.29 6.13
424 482 4.410400 GGGGGTGGAAGTCAGCGG 62.410 72.222 0.00 0.00 44.29 5.52
425 483 4.760047 CGGGGGTGGAAGTCAGCG 62.760 72.222 0.00 0.00 44.29 5.18
426 484 1.335132 TATCGGGGGTGGAAGTCAGC 61.335 60.000 0.00 0.00 42.74 4.26
427 485 1.139058 CTTATCGGGGGTGGAAGTCAG 59.861 57.143 0.00 0.00 0.00 3.51
428 486 1.200519 CTTATCGGGGGTGGAAGTCA 58.799 55.000 0.00 0.00 0.00 3.41
429 487 1.201424 ACTTATCGGGGGTGGAAGTC 58.799 55.000 0.00 0.00 0.00 3.01
432 490 2.911636 TGTAAACTTATCGGGGGTGGAA 59.088 45.455 0.00 0.00 0.00 3.53
437 495 2.273557 CGTGTGTAAACTTATCGGGGG 58.726 52.381 0.00 0.00 0.00 5.40
445 503 0.881600 GGGTCCGCGTGTGTAAACTT 60.882 55.000 4.92 0.00 0.00 2.66
446 504 1.301165 GGGTCCGCGTGTGTAAACT 60.301 57.895 4.92 0.00 0.00 2.66
457 515 1.299541 CAGTATTGTGATGGGTCCGC 58.700 55.000 0.00 0.00 0.00 5.54
478 536 1.129326 CGAGACGAGGTGTGTGAAAC 58.871 55.000 0.00 0.00 37.35 2.78
479 537 0.596600 GCGAGACGAGGTGTGTGAAA 60.597 55.000 0.00 0.00 0.00 2.69
480 538 1.007734 GCGAGACGAGGTGTGTGAA 60.008 57.895 0.00 0.00 0.00 3.18
481 539 0.604511 TAGCGAGACGAGGTGTGTGA 60.605 55.000 0.00 0.00 0.00 3.58
482 540 0.452184 ATAGCGAGACGAGGTGTGTG 59.548 55.000 0.00 0.00 0.00 3.82
499 557 3.006430 TGTCAAAGTCTTGGTCGCTCATA 59.994 43.478 0.00 0.00 33.01 2.15
501 559 1.138069 TGTCAAAGTCTTGGTCGCTCA 59.862 47.619 0.00 0.00 33.01 4.26
528 586 0.109597 GGTGCAATCTTTGTGAGCGG 60.110 55.000 0.00 0.00 0.00 5.52
530 588 2.352127 GGAAGGTGCAATCTTTGTGAGC 60.352 50.000 5.23 0.00 0.00 4.26
531 589 2.886523 TGGAAGGTGCAATCTTTGTGAG 59.113 45.455 5.23 0.00 0.00 3.51
532 590 2.942804 TGGAAGGTGCAATCTTTGTGA 58.057 42.857 5.23 0.00 0.00 3.58
533 591 3.318839 TCTTGGAAGGTGCAATCTTTGTG 59.681 43.478 5.23 0.00 0.00 3.33
535 593 4.589216 TTCTTGGAAGGTGCAATCTTTG 57.411 40.909 5.23 0.00 0.00 2.77
536 594 6.916360 TTATTCTTGGAAGGTGCAATCTTT 57.084 33.333 5.23 0.00 0.00 2.52
539 597 5.506317 CCGATTATTCTTGGAAGGTGCAATC 60.506 44.000 0.00 0.00 0.00 2.67
543 601 2.033424 GCCGATTATTCTTGGAAGGTGC 59.967 50.000 0.00 0.00 0.00 5.01
571 629 5.257082 ACCATTAAAGTGCGAGTGTTTTT 57.743 34.783 0.00 0.00 0.00 1.94
583 641 5.585820 AAACCGTGTCAAACCATTAAAGT 57.414 34.783 0.00 0.00 0.00 2.66
585 643 8.848182 ACTATTAAACCGTGTCAAACCATTAAA 58.152 29.630 0.00 0.00 0.00 1.52
586 644 8.393671 ACTATTAAACCGTGTCAAACCATTAA 57.606 30.769 0.00 0.00 0.00 1.40
588 646 6.887626 ACTATTAAACCGTGTCAAACCATT 57.112 33.333 0.00 0.00 0.00 3.16
590 648 6.696441 AAACTATTAAACCGTGTCAAACCA 57.304 33.333 0.00 0.00 0.00 3.67
591 649 6.638063 GGAAAACTATTAAACCGTGTCAAACC 59.362 38.462 0.00 0.00 0.00 3.27
592 650 7.420002 AGGAAAACTATTAAACCGTGTCAAAC 58.580 34.615 0.00 0.00 0.00 2.93
636 730 4.880537 CTGCCTAGCCCGCGTCAG 62.881 72.222 4.92 0.00 0.00 3.51
707 810 2.803817 GGCGGCGGGATTCCTTCTA 61.804 63.158 9.78 0.00 0.00 2.10
739 851 1.810030 GTTTAGGCCCTCGAGCACG 60.810 63.158 6.99 0.00 41.26 5.34
740 852 0.741221 CTGTTTAGGCCCTCGAGCAC 60.741 60.000 6.99 0.00 0.00 4.40
741 853 1.596934 CTGTTTAGGCCCTCGAGCA 59.403 57.895 6.99 0.00 0.00 4.26
742 854 1.815840 GCTGTTTAGGCCCTCGAGC 60.816 63.158 6.99 0.00 0.00 5.03
743 855 0.250513 AAGCTGTTTAGGCCCTCGAG 59.749 55.000 5.13 5.13 0.00 4.04
744 856 0.690762 AAAGCTGTTTAGGCCCTCGA 59.309 50.000 0.00 0.00 0.00 4.04
749 861 1.819288 GGGAAGAAAGCTGTTTAGGCC 59.181 52.381 0.00 0.00 0.00 5.19
763 875 0.467290 AGCAAAAAGGCGTGGGAAGA 60.467 50.000 0.00 0.00 39.27 2.87
792 904 1.298667 GGCGTGTGTGGGGATTAGT 59.701 57.895 0.00 0.00 0.00 2.24
804 938 2.561478 AGGTTTAGAACATGGCGTGT 57.439 45.000 6.51 6.51 44.84 4.49
805 939 3.502211 AGAAAGGTTTAGAACATGGCGTG 59.498 43.478 4.87 4.87 0.00 5.34
806 940 3.751518 AGAAAGGTTTAGAACATGGCGT 58.248 40.909 0.00 0.00 0.00 5.68
822 956 5.947228 TGCACTTGTGGAGAATAAGAAAG 57.053 39.130 2.81 0.00 31.72 2.62
829 963 1.615392 GGCTTTGCACTTGTGGAGAAT 59.385 47.619 2.81 0.00 0.00 2.40
831 965 0.183492 AGGCTTTGCACTTGTGGAGA 59.817 50.000 2.81 0.00 0.00 3.71
833 967 1.032014 GAAGGCTTTGCACTTGTGGA 58.968 50.000 0.00 0.00 0.00 4.02
834 968 0.032540 GGAAGGCTTTGCACTTGTGG 59.967 55.000 0.00 0.00 0.00 4.17
835 969 1.035139 AGGAAGGCTTTGCACTTGTG 58.965 50.000 0.00 0.00 0.00 3.33
836 970 1.780503 AAGGAAGGCTTTGCACTTGT 58.219 45.000 0.00 0.00 0.00 3.16
842 976 0.891373 GGGAGAAAGGAAGGCTTTGC 59.109 55.000 0.00 0.00 0.00 3.68
958 1111 1.127343 ATTGGGGTTGTTGTGGTTGG 58.873 50.000 0.00 0.00 0.00 3.77
979 1137 3.333804 TCTTGATCTTATGTGCGTTGCA 58.666 40.909 0.00 0.00 35.60 4.08
1011 1188 4.634703 TGCACCCGCGTCCATTGT 62.635 61.111 4.92 0.00 42.97 2.71
1131 1311 1.933765 TCCTCCTCCCTCTTAAGAGCT 59.066 52.381 24.58 0.00 40.75 4.09
1676 1859 1.229209 AGGAAGTCCTTGGCCTCGA 60.229 57.895 3.32 0.00 46.09 4.04
1699 1882 3.052082 CTGCCTGACCAAGCACCG 61.052 66.667 0.00 0.00 34.68 4.94
1938 2169 1.377463 CTCGTCGGAGTCCCACTCT 60.377 63.158 2.80 0.00 44.46 3.24
1941 2172 3.450115 CCCTCGTCGGAGTCCCAC 61.450 72.222 2.80 0.00 38.70 4.61
2122 2371 0.386352 TCGTACGTTTCTCCTGCGTG 60.386 55.000 16.05 0.00 39.31 5.34
2136 2388 0.029567 CGACTGGATCAGCCTCGTAC 59.970 60.000 0.00 0.00 37.63 3.67
2139 2391 0.738975 TAACGACTGGATCAGCCTCG 59.261 55.000 0.00 6.44 36.50 4.63
2165 2426 8.427774 CAGAAACAAAACTCTTCAAAAACTGAC 58.572 33.333 0.00 0.00 32.21 3.51
2203 2464 8.079203 TGTTTGCACTAACAATTTACTACATGG 58.921 33.333 1.43 0.00 35.22 3.66
2217 2481 5.263185 CAACACAGTACTGTTTGCACTAAC 58.737 41.667 25.89 0.00 42.83 2.34
2237 2588 4.735985 TGCATCAGTGATTATGTTGCAAC 58.264 39.130 22.83 22.83 45.50 4.17
2314 2668 3.056304 GAGCAGAATTATGAGCGGAGAC 58.944 50.000 3.77 0.00 0.00 3.36
2327 2681 0.749454 GTCGCAATGGGGAGCAGAAT 60.749 55.000 0.00 0.00 36.56 2.40
2349 2704 8.216453 CAGCCTAATTTTTCTTTGAATTCGTTG 58.784 33.333 0.04 0.00 0.00 4.10
2373 2766 2.629050 ATCGGATTCGGCGGACACAG 62.629 60.000 7.21 0.00 36.95 3.66
2374 2767 2.717044 ATCGGATTCGGCGGACACA 61.717 57.895 7.21 0.00 36.95 3.72
2375 2768 2.106332 ATCGGATTCGGCGGACAC 59.894 61.111 7.21 0.00 36.95 3.67
2379 2772 4.235762 ACCCATCGGATTCGGCGG 62.236 66.667 7.21 0.00 36.95 6.13
2381 2774 2.661866 CGACCCATCGGATTCGGC 60.662 66.667 0.00 0.00 44.99 5.54
2412 2811 8.773404 AGTTACTGTATGTGTGACCTAATTTC 57.227 34.615 0.00 0.00 0.00 2.17
2455 2870 1.340017 CGCTGGATTTCCTTTCCTCCA 60.340 52.381 0.00 0.00 36.40 3.86
2526 2953 2.971452 GTCGACCCGAGCCTTTCT 59.029 61.111 3.51 0.00 36.23 2.52
2570 2997 1.148157 CCATTCGAGCAGTACGCCTG 61.148 60.000 6.15 0.00 44.04 4.85
2571 2998 1.141881 CCATTCGAGCAGTACGCCT 59.858 57.895 6.15 0.00 44.04 5.52
2628 3058 2.295070 GCTGGACCCACGTAAAAACAAT 59.705 45.455 0.00 0.00 0.00 2.71
2820 3287 2.317609 CGGCACACCCACTCGAAAG 61.318 63.158 0.00 0.00 0.00 2.62
2838 3305 3.170585 GTACGTGTCGACTGCGCC 61.171 66.667 24.85 15.82 37.46 6.53
3025 3512 1.504359 CGTTTGCGGTTTCTAGTCCA 58.496 50.000 0.00 0.00 0.00 4.02
3066 3554 6.693545 TGTTTAAATTTCTCGCACGAAACAAT 59.306 30.769 8.46 0.00 35.88 2.71
3075 3563 5.181690 AGCTGTTGTTTAAATTTCTCGCA 57.818 34.783 0.00 0.00 0.00 5.10


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

AutoCloner maintained by Alex Coulton.