Multiple sequence alignment - TraesCS5A01G485300

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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 TraesCS5A01G485300 chr5A 100.000 3869 0 0 1 3869 656670012 656673880 0.000000e+00 7145.0
1 TraesCS5A01G485300 chr5A 94.428 2082 75 13 762 2825 656493907 656495965 0.000000e+00 3164.0
2 TraesCS5A01G485300 chr5A 90.291 1720 142 7 1067 2785 656222598 656220903 0.000000e+00 2228.0
3 TraesCS5A01G485300 chr5A 88.235 187 10 4 604 788 656493727 656493903 3.030000e-51 213.0
4 TraesCS5A01G485300 chr5B 93.640 2563 110 23 604 3144 665539262 665541793 0.000000e+00 3781.0
5 TraesCS5A01G485300 chr5B 93.079 2225 103 22 619 2831 665173656 665171471 0.000000e+00 3208.0
6 TraesCS5A01G485300 chr5B 89.988 1728 148 13 1067 2785 665026437 665024726 0.000000e+00 2209.0
7 TraesCS5A01G485300 chr5B 88.089 722 59 10 3156 3867 665542227 665542931 0.000000e+00 832.0
8 TraesCS5A01G485300 chr5D 93.166 2517 110 20 617 3125 528586776 528589238 0.000000e+00 3639.0
9 TraesCS5A01G485300 chr5D 94.874 2029 88 12 804 2825 528414969 528416988 0.000000e+00 3157.0
10 TraesCS5A01G485300 chr5D 89.769 1730 145 25 1067 2785 528296423 528294715 0.000000e+00 2185.0
11 TraesCS5A01G485300 chr7B 93.664 363 23 0 212 574 63772805 63773167 9.450000e-151 544.0
12 TraesCS5A01G485300 chr7B 86.199 442 56 4 1641 2078 706991894 706991454 1.260000e-129 473.0
13 TraesCS5A01G485300 chr7B 91.045 201 13 3 1 197 63772381 63772580 2.290000e-67 267.0
14 TraesCS5A01G485300 chr3D 94.757 267 14 0 78 344 347560142 347559876 2.150000e-112 416.0
15 TraesCS5A01G485300 chr3D 98.182 55 1 0 27 81 347561417 347561363 3.180000e-16 97.1
16 TraesCS5A01G485300 chr2D 80.033 611 56 21 1641 2239 645597822 645598378 3.620000e-105 392.0
17 TraesCS5A01G485300 chr3A 78.472 432 83 9 3443 3867 151698570 151698998 1.370000e-69 274.0
18 TraesCS5A01G485300 chr3B 78.608 388 76 7 3483 3867 393259895 393259512 2.310000e-62 250.0
19 TraesCS5A01G485300 chr3B 89.831 59 6 0 2443 2501 537434386 537434328 4.150000e-10 76.8
20 TraesCS5A01G485300 chr4D 75.826 484 90 18 3398 3866 393138221 393137750 1.810000e-53 220.0
21 TraesCS5A01G485300 chr2A 83.871 93 15 0 3775 3867 733356185 733356093 5.320000e-14 89.8
22 TraesCS5A01G485300 chrUn 94.643 56 3 0 1398 1453 100089775 100089830 1.910000e-13 87.9


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 TraesCS5A01G485300 chr5A 656670012 656673880 3868 False 7145.00 7145 100.0000 1 3869 1 chr5A.!!$F1 3868
1 TraesCS5A01G485300 chr5A 656220903 656222598 1695 True 2228.00 2228 90.2910 1067 2785 1 chr5A.!!$R1 1718
2 TraesCS5A01G485300 chr5A 656493727 656495965 2238 False 1688.50 3164 91.3315 604 2825 2 chr5A.!!$F2 2221
3 TraesCS5A01G485300 chr5B 665171471 665173656 2185 True 3208.00 3208 93.0790 619 2831 1 chr5B.!!$R2 2212
4 TraesCS5A01G485300 chr5B 665539262 665542931 3669 False 2306.50 3781 90.8645 604 3867 2 chr5B.!!$F1 3263
5 TraesCS5A01G485300 chr5B 665024726 665026437 1711 True 2209.00 2209 89.9880 1067 2785 1 chr5B.!!$R1 1718
6 TraesCS5A01G485300 chr5D 528586776 528589238 2462 False 3639.00 3639 93.1660 617 3125 1 chr5D.!!$F2 2508
7 TraesCS5A01G485300 chr5D 528414969 528416988 2019 False 3157.00 3157 94.8740 804 2825 1 chr5D.!!$F1 2021
8 TraesCS5A01G485300 chr5D 528294715 528296423 1708 True 2185.00 2185 89.7690 1067 2785 1 chr5D.!!$R1 1718
9 TraesCS5A01G485300 chr7B 63772381 63773167 786 False 405.50 544 92.3545 1 574 2 chr7B.!!$F1 573
10 TraesCS5A01G485300 chr3D 347559876 347561417 1541 True 256.55 416 96.4695 27 344 2 chr3D.!!$R1 317
11 TraesCS5A01G485300 chr2D 645597822 645598378 556 False 392.00 392 80.0330 1641 2239 1 chr2D.!!$F1 598

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
576 791 0.03582 CCAGCTGCCGTACCCTAAAA 60.036 55.0 8.66 0.0 0.0 1.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2873 3286 1.603172 CCCTTGGCATCGATCGTACTC 60.603 57.143 15.94 4.82 0.0 2.59 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
23 24 0.606673 GACCAACAGGAAGGAGCACC 60.607 60.000 0.00 0.00 0.00 5.01
25 26 1.371183 CAACAGGAAGGAGCACCGA 59.629 57.895 0.00 0.00 41.83 4.69
157 162 2.113860 GCAGTGGCTGTTAATCTCCA 57.886 50.000 0.00 0.00 36.96 3.86
197 202 2.591715 GCGTTGCCACACTCAGGT 60.592 61.111 0.00 0.00 0.00 4.00
231 446 5.707298 CAGACCAAAAAGAAAGATAGCCAGA 59.293 40.000 0.00 0.00 0.00 3.86
260 475 2.854214 CGCAGCTAGCTTCTTCGCG 61.854 63.158 25.62 25.62 42.61 5.87
268 483 1.080434 GCTTCTTCGCGTGGAGACT 60.080 57.895 6.43 0.00 0.00 3.24
269 484 0.667792 GCTTCTTCGCGTGGAGACTT 60.668 55.000 6.43 0.00 0.00 3.01
272 487 0.809385 TCTTCGCGTGGAGACTTAGG 59.191 55.000 1.85 0.00 0.00 2.69
290 505 1.876714 GCAGCAGCAATGCGGATTG 60.877 57.895 23.69 23.69 41.82 2.67
307 522 2.345991 GGCTGTTGTGCCGGACTA 59.654 61.111 5.05 0.00 43.74 2.59
355 570 1.600916 AGTCGTGCCTGAAAAGCCC 60.601 57.895 0.00 0.00 0.00 5.19
382 597 2.046285 GGGGATTGCAACGGGTGAG 61.046 63.158 0.00 0.00 0.00 3.51
436 651 2.202797 CCGTCGGATGTGAGGCTG 60.203 66.667 4.91 0.00 0.00 4.85
494 709 4.477975 GGCGGTCGTGACGGAGAG 62.478 72.222 4.70 0.00 34.05 3.20
495 710 3.735029 GCGGTCGTGACGGAGAGT 61.735 66.667 4.70 0.00 34.05 3.24
544 759 3.946950 CGTAGGAGCGTCATCATGT 57.053 52.632 0.00 0.00 0.00 3.21
545 760 1.481240 CGTAGGAGCGTCATCATGTG 58.519 55.000 0.00 0.00 0.00 3.21
546 761 1.858091 GTAGGAGCGTCATCATGTGG 58.142 55.000 0.00 0.00 0.00 4.17
547 762 1.409064 GTAGGAGCGTCATCATGTGGA 59.591 52.381 0.00 0.00 0.00 4.02
548 763 0.463204 AGGAGCGTCATCATGTGGAG 59.537 55.000 0.00 0.00 0.00 3.86
549 764 0.461548 GGAGCGTCATCATGTGGAGA 59.538 55.000 0.00 0.00 0.00 3.71
550 765 1.069823 GGAGCGTCATCATGTGGAGAT 59.930 52.381 0.00 0.00 0.00 2.75
551 766 2.484417 GGAGCGTCATCATGTGGAGATT 60.484 50.000 0.00 0.00 0.00 2.40
552 767 2.543012 GAGCGTCATCATGTGGAGATTG 59.457 50.000 0.00 0.00 0.00 2.67
553 768 2.093288 AGCGTCATCATGTGGAGATTGT 60.093 45.455 0.00 0.00 0.00 2.71
554 769 2.286294 GCGTCATCATGTGGAGATTGTC 59.714 50.000 0.00 0.00 0.00 3.18
555 770 2.537214 CGTCATCATGTGGAGATTGTCG 59.463 50.000 0.00 0.00 0.00 4.35
556 771 3.525537 GTCATCATGTGGAGATTGTCGT 58.474 45.455 0.00 0.00 0.00 4.34
557 772 3.553511 GTCATCATGTGGAGATTGTCGTC 59.446 47.826 0.00 0.00 0.00 4.20
558 773 2.672961 TCATGTGGAGATTGTCGTCC 57.327 50.000 0.00 0.00 0.00 4.79
559 774 1.899142 TCATGTGGAGATTGTCGTCCA 59.101 47.619 0.00 0.00 40.72 4.02
560 775 2.094026 TCATGTGGAGATTGTCGTCCAG 60.094 50.000 0.00 0.00 43.69 3.86
561 776 0.037326 TGTGGAGATTGTCGTCCAGC 60.037 55.000 0.00 0.00 43.69 4.85
562 777 0.247736 GTGGAGATTGTCGTCCAGCT 59.752 55.000 0.00 0.00 43.69 4.24
563 778 0.247460 TGGAGATTGTCGTCCAGCTG 59.753 55.000 6.78 6.78 37.96 4.24
564 779 1.086634 GGAGATTGTCGTCCAGCTGC 61.087 60.000 8.66 0.00 32.55 5.25
565 780 1.078848 AGATTGTCGTCCAGCTGCC 60.079 57.895 8.66 0.00 0.00 4.85
566 781 2.434884 ATTGTCGTCCAGCTGCCG 60.435 61.111 8.66 12.86 0.00 5.69
567 782 3.240134 ATTGTCGTCCAGCTGCCGT 62.240 57.895 19.31 2.49 0.00 5.68
568 783 1.884075 ATTGTCGTCCAGCTGCCGTA 61.884 55.000 19.31 10.26 0.00 4.02
569 784 2.506438 GTCGTCCAGCTGCCGTAC 60.506 66.667 19.31 13.74 0.00 3.67
570 785 3.755628 TCGTCCAGCTGCCGTACC 61.756 66.667 19.31 0.00 0.00 3.34
571 786 4.814294 CGTCCAGCTGCCGTACCC 62.814 72.222 8.66 0.00 0.00 3.69
572 787 3.391382 GTCCAGCTGCCGTACCCT 61.391 66.667 8.66 0.00 0.00 4.34
573 788 2.056223 GTCCAGCTGCCGTACCCTA 61.056 63.158 8.66 0.00 0.00 3.53
574 789 1.305465 TCCAGCTGCCGTACCCTAA 60.305 57.895 8.66 0.00 0.00 2.69
575 790 0.905809 TCCAGCTGCCGTACCCTAAA 60.906 55.000 8.66 0.00 0.00 1.85
576 791 0.035820 CCAGCTGCCGTACCCTAAAA 60.036 55.000 8.66 0.00 0.00 1.52
577 792 1.084289 CAGCTGCCGTACCCTAAAAC 58.916 55.000 0.00 0.00 0.00 2.43
578 793 0.390735 AGCTGCCGTACCCTAAAACG 60.391 55.000 0.00 0.00 38.80 3.60
584 799 2.000429 CGTACCCTAAAACGGACAGG 58.000 55.000 0.00 0.00 35.51 4.00
586 801 4.313819 CCCTAAAACGGACAGGGC 57.686 61.111 1.33 0.00 42.59 5.19
587 802 1.743995 CCCTAAAACGGACAGGGCG 60.744 63.158 1.33 0.00 42.59 6.13
588 803 1.294138 CCTAAAACGGACAGGGCGA 59.706 57.895 0.00 0.00 0.00 5.54
589 804 0.107848 CCTAAAACGGACAGGGCGAT 60.108 55.000 0.00 0.00 0.00 4.58
590 805 1.006832 CTAAAACGGACAGGGCGATG 58.993 55.000 0.00 0.00 0.00 3.84
591 806 0.322322 TAAAACGGACAGGGCGATGT 59.678 50.000 0.00 0.00 35.68 3.06
592 807 1.234615 AAAACGGACAGGGCGATGTG 61.235 55.000 0.00 0.00 32.25 3.21
593 808 2.107041 AAACGGACAGGGCGATGTGA 62.107 55.000 0.00 0.00 32.25 3.58
594 809 1.899437 AACGGACAGGGCGATGTGAT 61.899 55.000 0.00 0.00 32.25 3.06
595 810 1.153369 CGGACAGGGCGATGTGATT 60.153 57.895 0.00 0.00 32.25 2.57
596 811 0.744414 CGGACAGGGCGATGTGATTT 60.744 55.000 0.00 0.00 32.25 2.17
597 812 1.463674 GGACAGGGCGATGTGATTTT 58.536 50.000 0.00 0.00 32.25 1.82
598 813 1.401905 GGACAGGGCGATGTGATTTTC 59.598 52.381 0.00 0.00 32.25 2.29
599 814 1.062587 GACAGGGCGATGTGATTTTCG 59.937 52.381 0.00 0.00 38.37 3.46
600 815 0.378257 CAGGGCGATGTGATTTTCGG 59.622 55.000 0.00 0.00 35.93 4.30
664 881 6.482835 TGTGACACACTTCTGAAAATAAACG 58.517 36.000 3.56 0.00 35.11 3.60
692 932 1.463674 ATCGCCAACAAATCCCTCAC 58.536 50.000 0.00 0.00 0.00 3.51
789 1047 1.543358 TGCACACACAAACACACACAT 59.457 42.857 0.00 0.00 0.00 3.21
790 1048 1.919263 GCACACACAAACACACACATG 59.081 47.619 0.00 0.00 0.00 3.21
800 1076 4.890158 AACACACACATGGAGTATCTCA 57.110 40.909 0.00 0.00 33.73 3.27
930 1232 6.118170 CACCAAGAACCACAGATCAATCTAT 58.882 40.000 0.00 0.00 34.85 1.98
998 1303 0.537188 TGGAGAGAGGTTGATTCGGC 59.463 55.000 0.00 0.00 0.00 5.54
1064 1375 0.471617 GATGATGGGGAGTGGGACAG 59.528 60.000 0.00 0.00 41.80 3.51
1212 1532 2.526304 TTCTGTCTCTGTCCGTTTGG 57.474 50.000 0.00 0.00 0.00 3.28
1341 1683 1.303888 CCTCACCAAGGTGCTGCAT 60.304 57.895 14.35 0.00 45.04 3.96
1836 2187 2.693762 CGTTGTCTACCTCGCGGGA 61.694 63.158 8.08 0.92 38.76 5.14
1914 2265 2.161078 TTGTCGTGGCTGCGGTCATA 62.161 55.000 1.59 0.00 0.00 2.15
2544 2957 0.681887 TCTACGACCAGATGCCGGAA 60.682 55.000 5.05 0.00 0.00 4.30
2873 3286 1.226660 CCGCCGCTGCTTAATTTGG 60.227 57.895 0.00 0.00 34.43 3.28
2878 3291 2.223272 GCCGCTGCTTAATTTGGAGTAC 60.223 50.000 0.00 0.00 33.53 2.73
2911 3324 5.987953 CCAAGGGCATCATACATATAGATCG 59.012 44.000 0.00 0.00 0.00 3.69
2913 3326 7.201911 CCAAGGGCATCATACATATAGATCGTA 60.202 40.741 0.00 0.00 0.00 3.43
2914 3327 7.278461 AGGGCATCATACATATAGATCGTAC 57.722 40.000 0.00 0.00 0.00 3.67
2945 3358 4.094294 GTGATAATTAAGCTGGTGCGTGAA 59.906 41.667 0.00 0.00 45.42 3.18
2946 3359 4.697828 TGATAATTAAGCTGGTGCGTGAAA 59.302 37.500 0.00 0.00 45.42 2.69
2977 3391 9.640963 AGTTCAGTTGATAAACATGTACTACTC 57.359 33.333 0.00 0.00 0.00 2.59
2979 3393 7.255569 TCAGTTGATAAACATGTACTACTCCG 58.744 38.462 0.00 0.00 0.00 4.63
2980 3394 7.033791 CAGTTGATAAACATGTACTACTCCGT 58.966 38.462 0.00 0.00 0.00 4.69
2981 3395 8.186163 CAGTTGATAAACATGTACTACTCCGTA 58.814 37.037 0.00 0.00 0.00 4.02
2982 3396 8.910944 AGTTGATAAACATGTACTACTCCGTAT 58.089 33.333 0.00 0.00 0.00 3.06
2983 3397 8.965172 GTTGATAAACATGTACTACTCCGTATG 58.035 37.037 0.00 0.00 0.00 2.39
2984 3398 8.454570 TGATAAACATGTACTACTCCGTATGA 57.545 34.615 0.00 0.00 0.00 2.15
3054 3468 5.048713 AGTTTCCAAACTAATCCGAAGCTTG 60.049 40.000 2.10 0.00 46.75 4.01
3090 3507 7.414540 GCACCACTTAATAATCTTCTTGGACAG 60.415 40.741 0.00 0.00 0.00 3.51
3125 3542 0.895100 ATCAGCAAAAGCGCTTCCCA 60.895 50.000 25.24 4.89 41.38 4.37
3144 3561 3.909995 CCCATGTCCCCTTGTAGATCATA 59.090 47.826 0.00 0.00 0.00 2.15
3213 4052 9.857957 GTAGGAAATCACCTTGCTATATACTAC 57.142 37.037 0.00 0.00 41.00 2.73
3235 4074 0.031585 TCACCCTCGTTTGACTCGTG 59.968 55.000 0.00 0.00 0.00 4.35
3281 4120 8.453238 ACATACTCCTACTAGGCATATAATCG 57.547 38.462 0.00 0.00 34.61 3.34
3338 4188 5.183014 CATGATGAAAGATGTCATGGGTG 57.817 43.478 6.67 0.00 43.32 4.61
3339 4189 4.305539 TGATGAAAGATGTCATGGGTGT 57.694 40.909 0.00 0.00 38.38 4.16
3340 4190 4.011698 TGATGAAAGATGTCATGGGTGTG 58.988 43.478 0.00 0.00 38.38 3.82
3341 4191 3.507162 TGAAAGATGTCATGGGTGTGT 57.493 42.857 0.00 0.00 0.00 3.72
3370 4305 2.163211 GTCCGGCTCGTTTCTAGTTAGT 59.837 50.000 0.00 0.00 0.00 2.24
3378 4313 5.515626 GCTCGTTTCTAGTTAGTATGTGTGG 59.484 44.000 0.00 0.00 0.00 4.17
3455 4399 9.369672 ACAAAAGGGTAATCAAAATAGGTGTAA 57.630 29.630 0.00 0.00 0.00 2.41
3462 4406 6.469782 AATCAAAATAGGTGTAATGGCCAG 57.530 37.500 13.05 0.00 0.00 4.85
3507 4451 5.452078 TTTCAATTTTCACCTCGATGCTT 57.548 34.783 0.00 0.00 0.00 3.91
3509 4453 2.919229 CAATTTTCACCTCGATGCTTGC 59.081 45.455 0.00 0.00 0.00 4.01
3511 4455 2.760634 TTTCACCTCGATGCTTGCTA 57.239 45.000 0.00 0.00 0.00 3.49
3518 4462 3.118629 ACCTCGATGCTTGCTATTCTTGA 60.119 43.478 0.00 0.00 0.00 3.02
3519 4463 3.873361 CCTCGATGCTTGCTATTCTTGAA 59.127 43.478 0.00 0.00 0.00 2.69
3525 4469 6.238184 CGATGCTTGCTATTCTTGAATACACA 60.238 38.462 0.00 0.00 0.00 3.72
3535 4479 9.282247 CTATTCTTGAATACACAAATGAGTTGC 57.718 33.333 0.00 0.00 41.31 4.17
3567 4511 5.319043 TGGAAAAGAGAACCAAGGTATGT 57.681 39.130 0.00 0.00 0.00 2.29
3569 4513 6.843752 TGGAAAAGAGAACCAAGGTATGTTA 58.156 36.000 0.00 0.00 0.00 2.41
3571 4515 7.947890 TGGAAAAGAGAACCAAGGTATGTTAAT 59.052 33.333 0.00 0.00 0.00 1.40
3572 4516 8.244113 GGAAAAGAGAACCAAGGTATGTTAATG 58.756 37.037 0.00 0.00 0.00 1.90
3573 4517 6.759497 AAGAGAACCAAGGTATGTTAATGC 57.241 37.500 0.00 0.00 0.00 3.56
3574 4518 5.815581 AGAGAACCAAGGTATGTTAATGCA 58.184 37.500 0.00 0.00 0.00 3.96
3635 4579 1.554617 TGAGGTCTCATGGATGCGAAA 59.445 47.619 0.00 0.00 34.14 3.46
3665 4609 3.694072 TGCAAAGGTGATATTACTGTGCC 59.306 43.478 12.21 0.00 0.00 5.01
3709 4653 9.321562 GTTCCTTCACCAAACGATAATTATCTA 57.678 33.333 20.47 0.00 0.00 1.98
3719 4663 8.926710 CAAACGATAATTATCTACCTCATGGAC 58.073 37.037 20.47 0.00 37.04 4.02
3728 4672 1.933021 ACCTCATGGACGAACACCTA 58.067 50.000 0.00 0.00 37.04 3.08
3729 4673 2.467880 ACCTCATGGACGAACACCTAT 58.532 47.619 0.00 0.00 37.04 2.57
3736 4680 7.974501 CCTCATGGACGAACACCTATATATTAC 59.025 40.741 0.00 0.00 34.57 1.89
3740 4684 8.020777 TGGACGAACACCTATATATTACCAAA 57.979 34.615 0.00 0.00 0.00 3.28
3765 4709 8.964420 ATACAAATAATGTTTTGTCGTTCCAG 57.036 30.769 8.97 0.00 44.39 3.86
3812 4756 5.874895 TGATCAAATCACTGAAGAGCTTG 57.125 39.130 0.00 0.00 33.59 4.01
3838 4782 9.520204 GACAATTGGTTTGATGAGGTTAATATG 57.480 33.333 10.83 0.00 38.76 1.78
3839 4783 8.477256 ACAATTGGTTTGATGAGGTTAATATGG 58.523 33.333 10.83 0.00 38.76 2.74
3841 4785 7.880160 TTGGTTTGATGAGGTTAATATGGAG 57.120 36.000 0.00 0.00 0.00 3.86
3867 4811 7.408756 TTCTTATTAGCATGTTGGCTTTGAT 57.591 32.000 0.00 0.00 42.71 2.57
3868 4812 7.408756 TCTTATTAGCATGTTGGCTTTGATT 57.591 32.000 0.00 0.00 42.71 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
182 187 0.179045 AGTGACCTGAGTGTGGCAAC 60.179 55.000 0.00 0.00 0.00 4.17
197 202 5.110814 TCTTTTTGGTCTGAAAGGAGTGA 57.889 39.130 0.00 0.00 34.45 3.41
214 429 4.013050 GCTGGTCTGGCTATCTTTCTTTT 58.987 43.478 0.00 0.00 0.00 2.27
260 475 0.742635 GCTGCTGCCTAAGTCTCCAC 60.743 60.000 3.85 0.00 0.00 4.02
268 483 2.409055 CCGCATTGCTGCTGCCTAA 61.409 57.895 13.47 1.83 46.65 2.69
269 484 2.613660 ATCCGCATTGCTGCTGCCTA 62.614 55.000 13.47 1.46 46.65 3.93
272 487 1.876714 CAATCCGCATTGCTGCTGC 60.877 57.895 8.89 8.89 46.65 5.25
335 550 1.081840 GCTTTTCAGGCACGACTGC 60.082 57.895 0.00 0.00 43.41 4.40
355 570 3.530260 GCAATCCCCATGCCGGTG 61.530 66.667 1.90 0.00 37.85 4.94
368 583 2.489329 CAAGATTCTCACCCGTTGCAAT 59.511 45.455 0.59 0.00 0.00 3.56
382 597 2.474816 CGAATCCCTCGGACAAGATTC 58.525 52.381 0.00 0.00 44.20 2.52
436 651 4.222886 CGTCTCATCTCATTCCGTATGAC 58.777 47.826 0.00 0.00 38.35 3.06
477 692 4.477975 CTCTCCGTCACGACCGCC 62.478 72.222 0.00 0.00 0.00 6.13
516 731 4.514577 CTCCTACGGTGCGGGCTG 62.515 72.222 0.00 0.00 0.00 4.85
522 737 1.589196 GATGACGCTCCTACGGTGC 60.589 63.158 0.00 0.00 38.64 5.01
523 738 0.385751 ATGATGACGCTCCTACGGTG 59.614 55.000 0.00 0.00 37.37 4.94
524 739 0.385751 CATGATGACGCTCCTACGGT 59.614 55.000 0.00 0.00 37.37 4.83
525 740 0.385751 ACATGATGACGCTCCTACGG 59.614 55.000 0.00 0.00 37.37 4.02
526 741 1.481240 CACATGATGACGCTCCTACG 58.519 55.000 0.00 0.00 39.50 3.51
527 742 1.409064 TCCACATGATGACGCTCCTAC 59.591 52.381 0.00 0.00 0.00 3.18
528 743 1.683385 CTCCACATGATGACGCTCCTA 59.317 52.381 0.00 0.00 0.00 2.94
529 744 0.463204 CTCCACATGATGACGCTCCT 59.537 55.000 0.00 0.00 0.00 3.69
530 745 0.461548 TCTCCACATGATGACGCTCC 59.538 55.000 0.00 0.00 0.00 4.70
531 746 2.522836 ATCTCCACATGATGACGCTC 57.477 50.000 0.00 0.00 0.00 5.03
532 747 2.093288 ACAATCTCCACATGATGACGCT 60.093 45.455 0.00 0.00 0.00 5.07
533 748 2.283298 ACAATCTCCACATGATGACGC 58.717 47.619 0.00 0.00 0.00 5.19
534 749 2.537214 CGACAATCTCCACATGATGACG 59.463 50.000 0.00 0.00 0.00 4.35
535 750 3.525537 ACGACAATCTCCACATGATGAC 58.474 45.455 0.00 0.00 0.00 3.06
536 751 3.430790 GGACGACAATCTCCACATGATGA 60.431 47.826 0.00 0.00 0.00 2.92
537 752 2.868583 GGACGACAATCTCCACATGATG 59.131 50.000 0.00 0.00 0.00 3.07
538 753 2.501316 TGGACGACAATCTCCACATGAT 59.499 45.455 0.00 0.00 31.20 2.45
539 754 1.899142 TGGACGACAATCTCCACATGA 59.101 47.619 0.00 0.00 31.20 3.07
540 755 2.274437 CTGGACGACAATCTCCACATG 58.726 52.381 0.00 0.00 32.84 3.21
541 756 1.406069 GCTGGACGACAATCTCCACAT 60.406 52.381 0.00 0.00 32.84 3.21
542 757 0.037326 GCTGGACGACAATCTCCACA 60.037 55.000 0.00 0.00 32.84 4.17
543 758 0.247736 AGCTGGACGACAATCTCCAC 59.752 55.000 0.00 0.00 32.84 4.02
544 759 0.247460 CAGCTGGACGACAATCTCCA 59.753 55.000 5.57 0.00 35.20 3.86
545 760 1.086634 GCAGCTGGACGACAATCTCC 61.087 60.000 17.12 0.00 0.00 3.71
546 761 1.086634 GGCAGCTGGACGACAATCTC 61.087 60.000 17.12 0.00 0.00 2.75
547 762 1.078848 GGCAGCTGGACGACAATCT 60.079 57.895 17.12 0.00 0.00 2.40
548 763 3.490890 GGCAGCTGGACGACAATC 58.509 61.111 17.12 0.00 0.00 2.67
555 770 1.610554 TTAGGGTACGGCAGCTGGAC 61.611 60.000 17.12 8.27 0.00 4.02
556 771 0.905809 TTTAGGGTACGGCAGCTGGA 60.906 55.000 17.12 0.00 0.00 3.86
557 772 0.035820 TTTTAGGGTACGGCAGCTGG 60.036 55.000 17.12 1.57 0.00 4.85
558 773 1.084289 GTTTTAGGGTACGGCAGCTG 58.916 55.000 10.11 10.11 0.00 4.24
559 774 0.390735 CGTTTTAGGGTACGGCAGCT 60.391 55.000 0.00 0.00 34.30 4.24
560 775 2.084013 CGTTTTAGGGTACGGCAGC 58.916 57.895 0.00 0.00 34.30 5.25
565 780 1.404583 CCCTGTCCGTTTTAGGGTACG 60.405 57.143 0.00 0.00 45.00 3.67
566 781 2.391616 CCCTGTCCGTTTTAGGGTAC 57.608 55.000 0.00 0.00 45.00 3.34
570 785 0.107848 ATCGCCCTGTCCGTTTTAGG 60.108 55.000 0.00 0.00 0.00 2.69
571 786 1.006832 CATCGCCCTGTCCGTTTTAG 58.993 55.000 0.00 0.00 0.00 1.85
572 787 0.322322 ACATCGCCCTGTCCGTTTTA 59.678 50.000 0.00 0.00 0.00 1.52
573 788 1.072505 ACATCGCCCTGTCCGTTTT 59.927 52.632 0.00 0.00 0.00 2.43
574 789 1.671054 CACATCGCCCTGTCCGTTT 60.671 57.895 0.00 0.00 0.00 3.60
575 790 1.899437 ATCACATCGCCCTGTCCGTT 61.899 55.000 0.00 0.00 0.00 4.44
576 791 1.899437 AATCACATCGCCCTGTCCGT 61.899 55.000 0.00 0.00 0.00 4.69
577 792 0.744414 AAATCACATCGCCCTGTCCG 60.744 55.000 0.00 0.00 0.00 4.79
578 793 1.401905 GAAAATCACATCGCCCTGTCC 59.598 52.381 0.00 0.00 0.00 4.02
579 794 1.062587 CGAAAATCACATCGCCCTGTC 59.937 52.381 0.00 0.00 31.71 3.51
580 795 1.086696 CGAAAATCACATCGCCCTGT 58.913 50.000 0.00 0.00 31.71 4.00
581 796 0.378257 CCGAAAATCACATCGCCCTG 59.622 55.000 0.00 0.00 37.73 4.45
582 797 1.376609 GCCGAAAATCACATCGCCCT 61.377 55.000 0.00 0.00 37.73 5.19
583 798 1.064134 GCCGAAAATCACATCGCCC 59.936 57.895 0.00 0.00 37.73 6.13
584 799 1.261619 CTAGCCGAAAATCACATCGCC 59.738 52.381 0.00 0.00 37.73 5.54
585 800 1.333258 GCTAGCCGAAAATCACATCGC 60.333 52.381 2.29 0.00 37.73 4.58
586 801 2.205074 AGCTAGCCGAAAATCACATCG 58.795 47.619 12.13 0.00 38.74 3.84
587 802 2.545946 GGAGCTAGCCGAAAATCACATC 59.454 50.000 12.13 0.00 0.00 3.06
588 803 2.565841 GGAGCTAGCCGAAAATCACAT 58.434 47.619 12.13 0.00 0.00 3.21
589 804 2.024176 GGAGCTAGCCGAAAATCACA 57.976 50.000 12.13 0.00 0.00 3.58
599 814 3.724914 GACAGTGCCGGAGCTAGCC 62.725 68.421 12.13 2.59 40.80 3.93
600 815 1.384989 TAGACAGTGCCGGAGCTAGC 61.385 60.000 5.05 6.62 40.80 3.42
601 816 0.665835 CTAGACAGTGCCGGAGCTAG 59.334 60.000 5.05 1.97 40.80 3.42
602 817 0.752009 CCTAGACAGTGCCGGAGCTA 60.752 60.000 5.05 0.00 40.80 3.32
686 915 1.571919 GGAACGAATCGATGTGAGGG 58.428 55.000 10.55 0.00 0.00 4.30
692 932 3.165058 TCTTGAGGGAACGAATCGATG 57.835 47.619 10.55 0.00 0.00 3.84
789 1047 1.132453 CGTCGCTGTTGAGATACTCCA 59.868 52.381 0.00 0.00 0.00 3.86
790 1048 1.132643 ACGTCGCTGTTGAGATACTCC 59.867 52.381 0.00 0.00 0.00 3.85
800 1076 2.203153 AAAGGCCACGTCGCTGTT 60.203 55.556 5.01 0.00 0.00 3.16
930 1232 0.584396 CACTGCGCTTTTGGACGTAA 59.416 50.000 9.73 0.00 0.00 3.18
998 1303 1.523258 CCCTGCTGCTTCCTCATCG 60.523 63.158 0.00 0.00 0.00 3.84
1040 1351 0.464373 CCACTCCCCATCATCAACGG 60.464 60.000 0.00 0.00 0.00 4.44
1064 1375 1.677637 GGAGGAGTCGTCCACCCATC 61.678 65.000 23.92 0.00 45.63 3.51
1212 1532 1.732259 CACTGCCATCGACCAAAGTAC 59.268 52.381 0.00 0.00 0.00 2.73
1341 1683 1.596934 GGCGACCTTCATGTCCTGA 59.403 57.895 0.00 0.00 31.35 3.86
2873 3286 1.603172 CCCTTGGCATCGATCGTACTC 60.603 57.143 15.94 4.82 0.00 2.59
2902 3315 6.716898 TCACGAACGATGTACGATCTATAT 57.283 37.500 0.14 0.00 45.77 0.86
2908 3321 7.149015 GCTTAATTATCACGAACGATGTACGAT 60.149 37.037 0.14 0.00 45.77 3.73
2909 3322 6.141211 GCTTAATTATCACGAACGATGTACGA 59.859 38.462 0.14 0.00 45.77 3.43
2911 3324 7.274367 CAGCTTAATTATCACGAACGATGTAC 58.726 38.462 0.14 0.00 0.00 2.90
2913 3326 5.234329 CCAGCTTAATTATCACGAACGATGT 59.766 40.000 0.14 0.00 0.00 3.06
2914 3327 5.234329 ACCAGCTTAATTATCACGAACGATG 59.766 40.000 0.14 0.00 0.00 3.84
2977 3391 6.138088 TCGTCGATTACTAACAATCATACGG 58.862 40.000 15.05 4.10 40.62 4.02
2979 3393 7.533222 ACGATCGTCGATTACTAACAATCATAC 59.467 37.037 16.60 0.00 43.74 2.39
2980 3394 7.532884 CACGATCGTCGATTACTAACAATCATA 59.467 37.037 19.84 0.00 43.74 2.15
2981 3395 6.359883 CACGATCGTCGATTACTAACAATCAT 59.640 38.462 19.84 0.00 43.74 2.45
2982 3396 5.679792 CACGATCGTCGATTACTAACAATCA 59.320 40.000 19.84 0.00 43.74 2.57
2983 3397 5.680229 ACACGATCGTCGATTACTAACAATC 59.320 40.000 19.84 0.00 43.74 2.67
2984 3398 5.454554 CACACGATCGTCGATTACTAACAAT 59.545 40.000 19.84 0.00 43.74 2.71
3054 3468 1.588824 TAAGTGGTGCTGCATGCTGC 61.589 55.000 34.74 34.74 45.29 5.25
3090 3507 0.464373 TGATTTCAGCTGCCCGGATC 60.464 55.000 9.47 8.05 0.00 3.36
3115 3532 4.115199 GGGGACATGGGAAGCGCT 62.115 66.667 2.64 2.64 0.00 5.92
3116 3533 3.645268 AAGGGGACATGGGAAGCGC 62.645 63.158 0.00 0.00 0.00 5.92
3125 3542 3.006967 GCGTATGATCTACAAGGGGACAT 59.993 47.826 0.00 0.00 0.00 3.06
3144 3561 1.668047 GCACTCAAGTAACTACGGCGT 60.668 52.381 19.64 19.64 0.00 5.68
3213 4052 2.163815 ACGAGTCAAACGAGGGTGATAG 59.836 50.000 0.00 0.00 34.70 2.08
3216 4055 0.031585 CACGAGTCAAACGAGGGTGA 59.968 55.000 0.00 0.00 34.70 4.02
3217 4056 0.944311 CCACGAGTCAAACGAGGGTG 60.944 60.000 0.00 0.00 37.72 4.61
3218 4057 1.366366 CCACGAGTCAAACGAGGGT 59.634 57.895 0.00 0.00 37.72 4.34
3219 4058 0.249741 AACCACGAGTCAAACGAGGG 60.250 55.000 0.00 0.00 43.49 4.30
3260 4099 7.176490 ACTTCGATTATATGCCTAGTAGGAGT 58.824 38.462 21.02 9.48 37.67 3.85
3261 4100 7.633193 ACTTCGATTATATGCCTAGTAGGAG 57.367 40.000 21.02 6.03 37.67 3.69
3262 4101 8.418597 AAACTTCGATTATATGCCTAGTAGGA 57.581 34.615 21.02 5.63 37.67 2.94
3263 4102 8.926710 CAAAACTTCGATTATATGCCTAGTAGG 58.073 37.037 12.27 12.27 38.80 3.18
3264 4103 9.477484 ACAAAACTTCGATTATATGCCTAGTAG 57.523 33.333 0.00 0.00 0.00 2.57
3310 4160 9.239551 CCCATGACATCTTTCATCATGTTATAT 57.760 33.333 11.38 0.00 45.45 0.86
3333 4183 3.493830 GACTCGTCGCACACACCCA 62.494 63.158 0.00 0.00 0.00 4.51
3335 4185 2.733593 GGACTCGTCGCACACACC 60.734 66.667 0.00 0.00 0.00 4.16
3336 4186 3.097728 CGGACTCGTCGCACACAC 61.098 66.667 0.00 0.00 0.00 3.82
3337 4187 4.337060 CCGGACTCGTCGCACACA 62.337 66.667 0.00 0.00 33.95 3.72
3370 4305 1.552792 TCGAGGATTGTGCCACACATA 59.447 47.619 0.00 0.00 44.16 2.29
3441 4385 5.186256 TCTGGCCATTACACCTATTTTGA 57.814 39.130 5.51 0.00 0.00 2.69
3462 4406 7.617041 AAACATAGTAATGACTCAAAGGCTC 57.383 36.000 0.00 0.00 37.10 4.70
3492 4436 2.760634 TAGCAAGCATCGAGGTGAAA 57.239 45.000 0.00 0.00 0.00 2.69
3500 4444 6.132056 GTGTATTCAAGAATAGCAAGCATCG 58.868 40.000 2.88 0.00 34.27 3.84
3507 4451 8.565896 ACTCATTTGTGTATTCAAGAATAGCA 57.434 30.769 2.88 3.59 34.27 3.49
3509 4453 9.282247 GCAACTCATTTGTGTATTCAAGAATAG 57.718 33.333 2.88 0.00 37.54 1.73
3511 4455 7.092716 GGCAACTCATTTGTGTATTCAAGAAT 58.907 34.615 0.52 0.52 37.54 2.40
3535 4479 4.068599 GTTCTCTTTTCCAAGGAGTGAGG 58.931 47.826 12.03 0.00 0.00 3.86
3546 4490 7.754851 TTAACATACCTTGGTTCTCTTTTCC 57.245 36.000 0.00 0.00 0.00 3.13
3566 4510 7.138736 ACACTAACAAGTGACATTGCATTAAC 58.861 34.615 12.23 0.00 42.02 2.01
3567 4511 7.270757 ACACTAACAAGTGACATTGCATTAA 57.729 32.000 12.23 0.00 42.02 1.40
3569 4513 5.772825 ACACTAACAAGTGACATTGCATT 57.227 34.783 12.23 0.00 42.02 3.56
3571 4515 4.213270 GCTACACTAACAAGTGACATTGCA 59.787 41.667 12.23 0.00 42.02 4.08
3572 4516 4.213270 TGCTACACTAACAAGTGACATTGC 59.787 41.667 12.23 8.55 42.02 3.56
3573 4517 5.922739 TGCTACACTAACAAGTGACATTG 57.077 39.130 12.23 0.00 42.02 2.82
3574 4518 6.765989 TCTTTGCTACACTAACAAGTGACATT 59.234 34.615 12.23 0.00 42.02 2.71
3650 4594 4.503910 TGTCTGTGGCACAGTAATATCAC 58.496 43.478 38.27 28.76 46.03 3.06
3665 4609 3.366679 GGAACTTCAATGCCATGTCTGTG 60.367 47.826 0.00 0.00 0.00 3.66
3694 4638 7.813148 CGTCCATGAGGTAGATAATTATCGTTT 59.187 37.037 17.69 5.56 35.58 3.60
3695 4639 7.176165 TCGTCCATGAGGTAGATAATTATCGTT 59.824 37.037 17.69 6.20 35.58 3.85
3696 4640 6.657966 TCGTCCATGAGGTAGATAATTATCGT 59.342 38.462 17.69 10.15 35.58 3.73
3709 4653 1.933021 TAGGTGTTCGTCCATGAGGT 58.067 50.000 0.00 0.00 35.89 3.85
3747 4691 5.818336 TGTCTTCTGGAACGACAAAACATTA 59.182 36.000 0.00 0.00 34.99 1.90
3756 4700 6.388278 AGTTATACTTGTCTTCTGGAACGAC 58.612 40.000 0.00 0.00 0.00 4.34
3757 4701 6.585695 AGTTATACTTGTCTTCTGGAACGA 57.414 37.500 0.00 0.00 0.00 3.85
3812 4756 9.520204 CATATTAACCTCATCAAACCAATTGTC 57.480 33.333 4.43 0.00 40.11 3.18
3838 4782 5.358160 AGCCAACATGCTAATAAGAAACTCC 59.642 40.000 0.00 0.00 40.56 3.85
3839 4783 6.442513 AGCCAACATGCTAATAAGAAACTC 57.557 37.500 0.00 0.00 40.56 3.01
3841 4785 7.090173 TCAAAGCCAACATGCTAATAAGAAAC 58.910 34.615 0.00 0.00 41.80 2.78


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

AutoCloner maintained by Alex Coulton.