Multiple sequence alignment - TraesCS4D01G063200

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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 TraesCS4D01G063200 chr4D 100.000 2476 0 0 1 2476 39257553 39260028 0.000000e+00 4573
1 TraesCS4D01G063200 chr4D 82.536 773 124 10 1676 2446 309622892 309623655 0.000000e+00 669
2 TraesCS4D01G063200 chr4D 83.910 578 78 9 1678 2250 509018383 509018950 2.800000e-149 538
3 TraesCS4D01G063200 chr4D 91.489 141 9 2 1291 1431 39336329 39336466 9.040000e-45 191
4 TraesCS4D01G063200 chr4D 88.421 95 4 3 939 1033 461216371 461216458 9.360000e-20 108
5 TraesCS4D01G063200 chr4A 85.622 1078 103 22 1040 2103 561112489 561111450 0.000000e+00 1085
6 TraesCS4D01G063200 chr4A 87.238 478 30 15 449 907 561112955 561112490 1.310000e-142 516
7 TraesCS4D01G063200 chr4A 84.453 521 69 8 1761 2274 175003252 175003767 1.020000e-138 503
8 TraesCS4D01G063200 chr4A 93.939 99 5 1 449 547 561113923 561113826 5.520000e-32 148
9 TraesCS4D01G063200 chr4A 94.667 75 2 2 545 618 561113629 561113556 5.600000e-22 115
10 TraesCS4D01G063200 chr4B 91.077 594 40 6 1040 1629 57275063 57274479 0.000000e+00 791
11 TraesCS4D01G063200 chr4B 90.150 599 36 12 1040 1629 57279507 57278923 0.000000e+00 758
12 TraesCS4D01G063200 chr4B 88.756 587 31 16 1040 1600 57523865 57524442 0.000000e+00 686
13 TraesCS4D01G063200 chr4B 86.275 612 45 15 3 587 57275938 57275339 1.620000e-176 628
14 TraesCS4D01G063200 chr4B 80.752 665 44 27 1 587 57522928 57523586 2.260000e-120 442
15 TraesCS4D01G063200 chr4B 91.901 284 17 4 626 907 57523585 57523864 2.310000e-105 392
16 TraesCS4D01G063200 chr4B 90.426 282 22 3 626 907 57275340 57275064 1.400000e-97 366
17 TraesCS4D01G063200 chr4B 92.188 128 9 1 781 907 57279635 57279508 1.960000e-41 180
18 TraesCS4D01G063200 chr1D 82.832 798 128 9 1681 2476 414271550 414270760 0.000000e+00 706
19 TraesCS4D01G063200 chr1D 81.548 775 134 8 1705 2476 205085253 205086021 4.490000e-177 630
20 TraesCS4D01G063200 chr7D 82.134 778 128 10 1676 2446 517336828 517337601 0.000000e+00 656
21 TraesCS4D01G063200 chr3B 85.366 533 67 7 1770 2300 535698031 535697508 2.170000e-150 542
22 TraesCS4D01G063200 chr2A 82.055 613 101 8 1768 2378 125462486 125461881 4.720000e-142 514
23 TraesCS4D01G063200 chr2B 79.039 749 138 15 1682 2425 621178474 621177740 1.710000e-136 496
24 TraesCS4D01G063200 chr2B 77.163 705 119 30 1778 2476 796595855 796595187 3.010000e-99 372
25 TraesCS4D01G063200 chr2B 84.293 191 27 2 2235 2425 155201363 155201550 1.510000e-42 183
26 TraesCS4D01G063200 chr6A 93.478 138 8 1 905 1042 47486167 47486303 1.160000e-48 204
27 TraesCS4D01G063200 chr5D 93.846 130 6 2 910 1038 114902627 114902755 6.990000e-46 195
28 TraesCS4D01G063200 chr7B 90.345 145 12 2 900 1042 504811781 504811637 3.250000e-44 189
29 TraesCS4D01G063200 chr6B 92.126 127 10 0 910 1036 579548035 579547909 1.960000e-41 180
30 TraesCS4D01G063200 chr2D 89.231 130 12 2 910 1038 590418061 590418189 7.090000e-36 161


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 TraesCS4D01G063200 chr4D 39257553 39260028 2475 False 4573.000000 4573 100.000000 1 2476 1 chr4D.!!$F1 2475
1 TraesCS4D01G063200 chr4D 309622892 309623655 763 False 669.000000 669 82.536000 1676 2446 1 chr4D.!!$F3 770
2 TraesCS4D01G063200 chr4D 509018383 509018950 567 False 538.000000 538 83.910000 1678 2250 1 chr4D.!!$F5 572
3 TraesCS4D01G063200 chr4A 175003252 175003767 515 False 503.000000 503 84.453000 1761 2274 1 chr4A.!!$F1 513
4 TraesCS4D01G063200 chr4A 561111450 561113923 2473 True 466.000000 1085 90.366500 449 2103 4 chr4A.!!$R1 1654
5 TraesCS4D01G063200 chr4B 57274479 57279635 5156 True 544.600000 791 90.023200 3 1629 5 chr4B.!!$R1 1626
6 TraesCS4D01G063200 chr4B 57522928 57524442 1514 False 506.666667 686 87.136333 1 1600 3 chr4B.!!$F1 1599
7 TraesCS4D01G063200 chr1D 414270760 414271550 790 True 706.000000 706 82.832000 1681 2476 1 chr1D.!!$R1 795
8 TraesCS4D01G063200 chr1D 205085253 205086021 768 False 630.000000 630 81.548000 1705 2476 1 chr1D.!!$F1 771
9 TraesCS4D01G063200 chr7D 517336828 517337601 773 False 656.000000 656 82.134000 1676 2446 1 chr7D.!!$F1 770
10 TraesCS4D01G063200 chr3B 535697508 535698031 523 True 542.000000 542 85.366000 1770 2300 1 chr3B.!!$R1 530
11 TraesCS4D01G063200 chr2A 125461881 125462486 605 True 514.000000 514 82.055000 1768 2378 1 chr2A.!!$R1 610
12 TraesCS4D01G063200 chr2B 621177740 621178474 734 True 496.000000 496 79.039000 1682 2425 1 chr2B.!!$R1 743
13 TraesCS4D01G063200 chr2B 796595187 796595855 668 True 372.000000 372 77.163000 1778 2476 1 chr2B.!!$R2 698

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
349 4093 0.034756 ACAATACCGCAGTGTGCTGA 59.965 50.0 0.0 0.0 45.28 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1976 5828 0.533755 GCCGGCCGTAGACTAGTCTA 60.534 60.0 25.58 25.58 40.93 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
35 3731 5.058008 CGCGAACATTTTTGTAGATCACAAC 59.942 40.000 0.00 0.00 46.80 3.32
36 3732 6.142817 GCGAACATTTTTGTAGATCACAACT 58.857 36.000 9.36 0.00 46.80 3.16
37 3733 6.086765 GCGAACATTTTTGTAGATCACAACTG 59.913 38.462 9.36 9.70 46.80 3.16
229 3944 6.432802 AATTGCGAACATTTTCTAAACGTG 57.567 33.333 0.00 0.00 0.00 4.49
271 3986 8.050778 TGGTGGCAGTATTTTAACATAAGAAG 57.949 34.615 0.00 0.00 0.00 2.85
279 4023 5.873179 TTTTAACATAAGAAGCAGGTCGG 57.127 39.130 0.00 0.00 0.00 4.79
349 4093 0.034756 ACAATACCGCAGTGTGCTGA 59.965 50.000 0.00 0.00 45.28 4.26
368 4112 2.100197 GACCCATTTTAGGTTCCAGCC 58.900 52.381 0.00 0.00 37.88 4.85
388 4139 1.197721 CCAGTGCGATTGGTGACTTTC 59.802 52.381 0.00 0.00 0.00 2.62
396 4147 1.444119 TTGGTGACTTTCCAGCGCAC 61.444 55.000 11.47 0.00 37.36 5.34
544 4341 2.547640 GATGCTTCCCTGGCTGCTCA 62.548 60.000 0.00 0.00 0.00 4.26
547 4344 1.871126 GCTTCCCTGGCTGCTCAAAC 61.871 60.000 0.00 0.00 0.00 2.93
573 4370 0.245539 CTGCATGGCACTTGGGAAAG 59.754 55.000 0.00 0.00 33.79 2.62
597 4399 1.885887 TCAGTGGTGCTGGTTAATTGC 59.114 47.619 0.00 0.00 45.08 3.56
622 4424 1.926108 ACTAAGACAGTCTCCCGCTT 58.074 50.000 2.72 0.00 28.33 4.68
624 4426 1.819288 CTAAGACAGTCTCCCGCTTGA 59.181 52.381 2.72 0.00 0.00 3.02
626 4428 1.446966 GACAGTCTCCCGCTTGAGC 60.447 63.158 0.00 0.00 37.78 4.26
717 4519 4.620609 CGGCGATCTCTTCATCAAATCTAG 59.379 45.833 0.00 0.00 0.00 2.43
718 4520 4.388469 GGCGATCTCTTCATCAAATCTAGC 59.612 45.833 0.00 0.00 0.00 3.42
719 4521 4.987285 GCGATCTCTTCATCAAATCTAGCA 59.013 41.667 0.00 0.00 0.00 3.49
768 4572 2.747855 GGGGGAAAGTGCAGAGCG 60.748 66.667 0.00 0.00 0.00 5.03
907 4711 2.802667 CGCCACGCCAGAGATTTCG 61.803 63.158 0.00 0.00 0.00 3.46
908 4712 1.447838 GCCACGCCAGAGATTTCGA 60.448 57.895 0.00 0.00 0.00 3.71
909 4713 1.424493 GCCACGCCAGAGATTTCGAG 61.424 60.000 0.00 0.00 0.00 4.04
910 4714 0.807667 CCACGCCAGAGATTTCGAGG 60.808 60.000 0.00 0.00 0.00 4.63
911 4715 1.153549 ACGCCAGAGATTTCGAGGC 60.154 57.895 11.24 11.24 42.40 4.70
912 4716 1.884926 CGCCAGAGATTTCGAGGCC 60.885 63.158 14.29 0.00 42.67 5.19
913 4717 1.884926 GCCAGAGATTTCGAGGCCG 60.885 63.158 10.44 0.00 40.98 6.13
914 4718 1.517832 CCAGAGATTTCGAGGCCGT 59.482 57.895 0.00 0.00 37.05 5.68
915 4719 0.108138 CCAGAGATTTCGAGGCCGTT 60.108 55.000 0.00 0.00 37.05 4.44
916 4720 1.281899 CAGAGATTTCGAGGCCGTTC 58.718 55.000 0.00 0.00 37.05 3.95
917 4721 0.179134 AGAGATTTCGAGGCCGTTCG 60.179 55.000 8.05 8.05 41.79 3.95
918 4722 0.179145 GAGATTTCGAGGCCGTTCGA 60.179 55.000 12.70 12.70 46.86 3.71
923 4727 2.745728 TCGAGGCCGTTCGAAATTC 58.254 52.632 14.18 0.00 45.69 2.17
924 4728 0.738412 TCGAGGCCGTTCGAAATTCC 60.738 55.000 14.18 0.72 45.69 3.01
925 4729 1.017177 CGAGGCCGTTCGAAATTCCA 61.017 55.000 8.66 0.00 43.03 3.53
926 4730 0.446616 GAGGCCGTTCGAAATTCCAC 59.553 55.000 0.00 0.00 0.00 4.02
927 4731 0.958876 AGGCCGTTCGAAATTCCACC 60.959 55.000 0.00 0.00 0.00 4.61
928 4732 1.238625 GGCCGTTCGAAATTCCACCA 61.239 55.000 0.00 0.00 0.00 4.17
929 4733 0.168128 GCCGTTCGAAATTCCACCAG 59.832 55.000 0.00 0.00 0.00 4.00
930 4734 0.168128 CCGTTCGAAATTCCACCAGC 59.832 55.000 0.00 0.00 0.00 4.85
931 4735 1.156736 CGTTCGAAATTCCACCAGCT 58.843 50.000 0.00 0.00 0.00 4.24
932 4736 1.128692 CGTTCGAAATTCCACCAGCTC 59.871 52.381 0.00 0.00 0.00 4.09
933 4737 1.468914 GTTCGAAATTCCACCAGCTCC 59.531 52.381 0.00 0.00 0.00 4.70
934 4738 0.391130 TCGAAATTCCACCAGCTCCG 60.391 55.000 0.00 0.00 0.00 4.63
935 4739 1.369091 CGAAATTCCACCAGCTCCGG 61.369 60.000 0.00 0.00 0.00 5.14
936 4740 0.035439 GAAATTCCACCAGCTCCGGA 60.035 55.000 2.93 2.93 0.00 5.14
937 4741 0.035056 AAATTCCACCAGCTCCGGAG 60.035 55.000 27.83 27.83 0.00 4.63
938 4742 0.909610 AATTCCACCAGCTCCGGAGA 60.910 55.000 35.69 11.92 0.00 3.71
939 4743 1.333636 ATTCCACCAGCTCCGGAGAG 61.334 60.000 35.69 24.39 43.57 3.20
966 4770 3.474806 CAGTAAACTGGCGCTCCG 58.525 61.111 7.64 0.00 40.20 4.63
978 4782 3.773117 CGCTCCGCAAATTTCAACT 57.227 47.368 0.00 0.00 0.00 3.16
979 4783 2.892373 CGCTCCGCAAATTTCAACTA 57.108 45.000 0.00 0.00 0.00 2.24
980 4784 3.405170 CGCTCCGCAAATTTCAACTAT 57.595 42.857 0.00 0.00 0.00 2.12
981 4785 4.530094 CGCTCCGCAAATTTCAACTATA 57.470 40.909 0.00 0.00 0.00 1.31
982 4786 4.904116 CGCTCCGCAAATTTCAACTATAA 58.096 39.130 0.00 0.00 0.00 0.98
983 4787 4.728608 CGCTCCGCAAATTTCAACTATAAC 59.271 41.667 0.00 0.00 0.00 1.89
984 4788 5.447279 CGCTCCGCAAATTTCAACTATAACT 60.447 40.000 0.00 0.00 0.00 2.24
985 4789 5.965918 GCTCCGCAAATTTCAACTATAACTC 59.034 40.000 0.00 0.00 0.00 3.01
986 4790 6.431198 TCCGCAAATTTCAACTATAACTCC 57.569 37.500 0.00 0.00 0.00 3.85
987 4791 5.941058 TCCGCAAATTTCAACTATAACTCCA 59.059 36.000 0.00 0.00 0.00 3.86
988 4792 6.027749 CCGCAAATTTCAACTATAACTCCAC 58.972 40.000 0.00 0.00 0.00 4.02
989 4793 6.027749 CGCAAATTTCAACTATAACTCCACC 58.972 40.000 0.00 0.00 0.00 4.61
990 4794 6.348950 CGCAAATTTCAACTATAACTCCACCA 60.349 38.462 0.00 0.00 0.00 4.17
991 4795 7.029563 GCAAATTTCAACTATAACTCCACCAG 58.970 38.462 0.00 0.00 0.00 4.00
992 4796 6.759497 AATTTCAACTATAACTCCACCAGC 57.241 37.500 0.00 0.00 0.00 4.85
993 4797 5.499004 TTTCAACTATAACTCCACCAGCT 57.501 39.130 0.00 0.00 0.00 4.24
994 4798 4.737855 TCAACTATAACTCCACCAGCTC 57.262 45.455 0.00 0.00 0.00 4.09
995 4799 3.451178 TCAACTATAACTCCACCAGCTCC 59.549 47.826 0.00 0.00 0.00 4.70
996 4800 3.406512 ACTATAACTCCACCAGCTCCT 57.593 47.619 0.00 0.00 0.00 3.69
997 4801 3.034635 ACTATAACTCCACCAGCTCCTG 58.965 50.000 0.00 0.00 0.00 3.86
1007 4811 3.877951 CAGCTCCTGGAATGAAGCT 57.122 52.632 0.00 0.00 45.65 3.74
1008 4812 3.877951 AGCTCCTGGAATGAAGCTG 57.122 52.632 6.59 0.00 43.21 4.24
1009 4813 0.990374 AGCTCCTGGAATGAAGCTGT 59.010 50.000 6.59 0.00 43.21 4.40
1010 4814 1.093159 GCTCCTGGAATGAAGCTGTG 58.907 55.000 0.00 0.00 0.00 3.66
1011 4815 1.747709 CTCCTGGAATGAAGCTGTGG 58.252 55.000 0.00 0.00 0.00 4.17
1012 4816 1.280133 CTCCTGGAATGAAGCTGTGGA 59.720 52.381 0.00 0.00 0.00 4.02
1013 4817 1.280133 TCCTGGAATGAAGCTGTGGAG 59.720 52.381 0.00 0.00 0.00 3.86
1014 4818 1.093159 CTGGAATGAAGCTGTGGAGC 58.907 55.000 0.00 0.00 46.64 4.70
1022 4826 4.187056 GCTGTGGAGCGAAGTACC 57.813 61.111 0.00 0.00 34.87 3.34
1023 4827 1.592223 GCTGTGGAGCGAAGTACCT 59.408 57.895 0.00 0.00 34.87 3.08
1024 4828 0.458716 GCTGTGGAGCGAAGTACCTC 60.459 60.000 0.00 0.00 34.87 3.85
1025 4829 0.173708 CTGTGGAGCGAAGTACCTCC 59.826 60.000 8.52 8.52 46.25 4.30
1027 4831 3.915575 GGAGCGAAGTACCTCCGA 58.084 61.111 0.79 0.00 38.38 4.55
1028 4832 2.187073 GGAGCGAAGTACCTCCGAA 58.813 57.895 0.79 0.00 38.38 4.30
1029 4833 0.179142 GGAGCGAAGTACCTCCGAAC 60.179 60.000 0.79 0.00 38.38 3.95
1030 4834 0.524862 GAGCGAAGTACCTCCGAACA 59.475 55.000 3.75 0.00 0.00 3.18
1031 4835 0.526662 AGCGAAGTACCTCCGAACAG 59.473 55.000 3.75 0.00 0.00 3.16
1032 4836 0.458025 GCGAAGTACCTCCGAACAGG 60.458 60.000 3.75 0.00 42.97 4.00
1033 4837 0.172803 CGAAGTACCTCCGAACAGGG 59.827 60.000 0.00 0.00 41.52 4.45
1034 4838 0.108281 GAAGTACCTCCGAACAGGGC 60.108 60.000 0.00 0.00 41.52 5.19
1035 4839 1.551019 AAGTACCTCCGAACAGGGCC 61.551 60.000 0.00 0.00 41.52 5.80
1036 4840 1.988406 GTACCTCCGAACAGGGCCT 60.988 63.158 0.00 0.00 41.52 5.19
1037 4841 0.685458 GTACCTCCGAACAGGGCCTA 60.685 60.000 5.28 0.00 41.52 3.93
1038 4842 0.263765 TACCTCCGAACAGGGCCTAT 59.736 55.000 5.28 0.00 41.52 2.57
1073 4879 1.001746 ACTCTATGCATCCATGGCTCG 59.998 52.381 6.96 0.00 32.85 5.03
1098 4904 3.764885 ACTGAAAGCACACACAAAGAC 57.235 42.857 0.00 0.00 37.60 3.01
1099 4905 3.081061 ACTGAAAGCACACACAAAGACA 58.919 40.909 0.00 0.00 37.60 3.41
1100 4906 3.505680 ACTGAAAGCACACACAAAGACAA 59.494 39.130 0.00 0.00 37.60 3.18
1101 4907 4.095410 TGAAAGCACACACAAAGACAAG 57.905 40.909 0.00 0.00 0.00 3.16
1102 4908 3.755905 TGAAAGCACACACAAAGACAAGA 59.244 39.130 0.00 0.00 0.00 3.02
1146 4953 0.960364 TTTCCGCCATGAAGCTGTCC 60.960 55.000 0.00 0.00 0.00 4.02
1197 5013 2.096909 GTCCATCGTAAATTCGCATCCG 60.097 50.000 0.00 0.00 0.00 4.18
1198 5014 1.194547 CCATCGTAAATTCGCATCCGG 59.805 52.381 0.00 0.00 34.56 5.14
1241 5070 7.836512 TCTTTTTGACAAATTTTGTATGCGTC 58.163 30.769 14.49 2.60 45.52 5.19
1519 5352 4.006319 GAGTTCAATAAGGCTCTGCAAGT 58.994 43.478 0.00 0.00 33.76 3.16
1530 5363 2.851008 GCTCTGCAAGTTTGTTGTCGAC 60.851 50.000 9.11 9.11 33.76 4.20
1531 5364 2.609459 CTCTGCAAGTTTGTTGTCGACT 59.391 45.455 17.92 0.00 33.76 4.18
1532 5365 2.351418 TCTGCAAGTTTGTTGTCGACTG 59.649 45.455 17.92 4.95 33.76 3.51
1574 5407 4.278419 GTCTCTGGTTTGGCAGTGTAATTT 59.722 41.667 0.00 0.00 0.00 1.82
1578 5411 5.830991 TCTGGTTTGGCAGTGTAATTTAACT 59.169 36.000 0.00 0.00 0.00 2.24
1605 5439 4.490890 CACGCTTCGAATAAAATTTCCGAC 59.509 41.667 0.00 0.00 0.00 4.79
1617 5451 8.925161 ATAAAATTTCCGACCATAATGTGTTG 57.075 30.769 0.00 0.00 0.00 3.33
1672 5512 8.240267 AGAGATTTTACAGTACCCTGATACTC 57.760 38.462 0.00 0.00 41.50 2.59
1673 5513 8.062536 AGAGATTTTACAGTACCCTGATACTCT 58.937 37.037 0.00 0.00 41.50 3.24
1679 5519 8.632906 TTACAGTACCCTGATACTCTATAAGC 57.367 38.462 0.00 0.00 41.50 3.09
1710 5551 2.734276 GGCAACCCGCAAATTTCTTA 57.266 45.000 0.00 0.00 45.17 2.10
1718 5559 2.097466 CCGCAAATTTCTTACCGCATCT 59.903 45.455 0.00 0.00 0.00 2.90
1724 5567 6.294176 GCAAATTTCTTACCGCATCTATCCAT 60.294 38.462 0.00 0.00 0.00 3.41
1728 5571 4.096681 TCTTACCGCATCTATCCATGGAT 58.903 43.478 29.66 29.66 38.54 3.41
1738 5582 1.362224 ATCCATGGATAAGGGGACCG 58.638 55.000 26.25 0.00 43.80 4.79
1936 5788 4.742438 AAGGTAAAACTATGTGCACGTG 57.258 40.909 21.92 12.28 0.00 4.49
1970 5822 2.735762 GCTTCACTCCTATGACACGGAC 60.736 54.545 0.00 0.00 0.00 4.79
1971 5823 2.509166 TCACTCCTATGACACGGACT 57.491 50.000 0.00 0.00 0.00 3.85
1973 5825 3.276857 TCACTCCTATGACACGGACTAC 58.723 50.000 0.00 0.00 0.00 2.73
1975 5827 3.015327 ACTCCTATGACACGGACTACAC 58.985 50.000 0.00 0.00 0.00 2.90
1976 5828 3.280295 CTCCTATGACACGGACTACACT 58.720 50.000 0.00 0.00 0.00 3.55
1977 5829 4.080695 ACTCCTATGACACGGACTACACTA 60.081 45.833 0.00 0.00 0.00 2.74
1997 5850 3.603671 CTAGTCTACGGCCGGCCC 61.604 72.222 39.24 24.72 0.00 5.80
2011 5864 4.570874 GCCCTGGCGGATCCCTTC 62.571 72.222 6.06 0.00 0.00 3.46
2030 5883 1.299976 GTCTTTCCCATGTCCGGCT 59.700 57.895 0.00 0.00 0.00 5.52
2049 5904 1.140375 GCCCACTAACCGGACTACG 59.860 63.158 9.46 0.00 43.80 3.51
2060 5915 0.964358 CGGACTACGGGGAGTCTTGT 60.964 60.000 10.70 0.00 44.50 3.16
2062 5917 2.450476 GGACTACGGGGAGTCTTGTAA 58.550 52.381 10.70 0.00 44.50 2.41
2075 5930 6.823689 GGGAGTCTTGTAAGCATATTCTTTCA 59.176 38.462 0.00 0.00 0.00 2.69
2160 6018 1.371558 GAAGGTGCTTCCGTGGAGT 59.628 57.895 0.00 0.00 41.99 3.85
2176 6034 1.841302 GAGTCCAGATGGGTGTGCCA 61.841 60.000 0.00 0.00 38.11 4.92
2178 6036 1.074775 TCCAGATGGGTGTGCCAAC 59.925 57.895 0.00 0.00 38.11 3.77
2212 6070 0.762418 AAGACCGGACATGTCACCAA 59.238 50.000 26.47 0.00 35.15 3.67
2269 6127 2.895372 GATACAAGCGGTGGCGGG 60.895 66.667 0.00 0.00 46.35 6.13
2323 6181 4.927782 GCGTGGATATGCGGGCCA 62.928 66.667 4.39 0.00 0.00 5.36
2392 6250 2.883730 GGCTACGTGCGCATCGAA 60.884 61.111 29.62 10.96 44.05 3.71
2395 6253 1.226575 CTACGTGCGCATCGAAGGA 60.227 57.895 29.62 15.35 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 3706 4.449405 TGTGATCTACAAAAATGTTCGCGA 59.551 37.500 3.71 3.71 36.06 5.87
229 3944 7.602265 ACTGCCACCAAATTTAAATATGTTCAC 59.398 33.333 0.01 0.00 0.00 3.18
247 3962 6.972901 GCTTCTTATGTTAAAATACTGCCACC 59.027 38.462 0.00 0.00 0.00 4.61
349 4093 1.273041 GGGCTGGAACCTAAAATGGGT 60.273 52.381 0.00 0.00 38.94 4.51
368 4112 1.197721 GAAAGTCACCAATCGCACTGG 59.802 52.381 0.00 0.00 40.05 4.00
407 4158 1.966451 ACAAAGGCTCCTTTCCGCG 60.966 57.895 10.76 0.00 43.56 6.46
408 4159 1.581447 CACAAAGGCTCCTTTCCGC 59.419 57.895 10.76 0.00 43.56 5.54
409 4160 1.581447 GCACAAAGGCTCCTTTCCG 59.419 57.895 10.76 6.58 43.56 4.30
410 4161 1.172812 ACGCACAAAGGCTCCTTTCC 61.173 55.000 10.76 2.89 43.56 3.13
411 4162 0.238553 GACGCACAAAGGCTCCTTTC 59.761 55.000 10.76 0.52 43.56 2.62
412 4163 1.507141 CGACGCACAAAGGCTCCTTT 61.507 55.000 8.04 8.04 45.98 3.11
413 4164 1.961277 CGACGCACAAAGGCTCCTT 60.961 57.895 0.00 0.00 37.98 3.36
470 4254 9.855021 AATAGAAATACAAATGGAAAAGGTTCG 57.145 29.630 0.00 0.00 34.28 3.95
517 4301 1.094073 CAGGGAAGCATCCTCGCAAG 61.094 60.000 8.09 0.00 45.77 4.01
544 4341 2.154462 GTGCCATGCAGACACTAGTTT 58.846 47.619 8.77 0.00 40.08 2.66
547 4344 1.736126 CAAGTGCCATGCAGACACTAG 59.264 52.381 16.61 0.00 43.63 2.57
567 4364 1.168714 GCACCACTGATCACTTTCCC 58.831 55.000 0.00 0.00 0.00 3.97
597 4399 3.063725 CGGGAGACTGTCTTAGTTACTCG 59.936 52.174 12.27 5.82 40.53 4.18
622 4424 0.618458 AAACGCTAGGGATTGGCTCA 59.382 50.000 14.59 0.00 0.00 4.26
624 4426 1.463674 CAAAACGCTAGGGATTGGCT 58.536 50.000 14.59 0.00 0.00 4.75
695 4497 4.388469 GCTAGATTTGATGAAGAGATCGCC 59.612 45.833 0.00 0.00 0.00 5.54
719 4521 2.143925 GAAGCGGCTAACAGTTTCACT 58.856 47.619 1.35 0.00 0.00 3.41
768 4572 3.414700 CTGACCCGAACAGTGCGC 61.415 66.667 0.00 0.00 0.00 6.09
875 4679 2.095213 GCGTGGCGATTTCATTGACTTA 59.905 45.455 0.00 0.00 0.00 2.24
907 4711 0.446616 GTGGAATTTCGAACGGCCTC 59.553 55.000 0.00 0.00 0.00 4.70
908 4712 0.958876 GGTGGAATTTCGAACGGCCT 60.959 55.000 0.00 0.00 0.00 5.19
909 4713 1.238625 TGGTGGAATTTCGAACGGCC 61.239 55.000 0.00 0.00 0.00 6.13
910 4714 0.168128 CTGGTGGAATTTCGAACGGC 59.832 55.000 0.00 0.00 0.00 5.68
911 4715 0.168128 GCTGGTGGAATTTCGAACGG 59.832 55.000 0.00 1.20 0.00 4.44
912 4716 1.128692 GAGCTGGTGGAATTTCGAACG 59.871 52.381 0.00 0.00 0.00 3.95
913 4717 1.468914 GGAGCTGGTGGAATTTCGAAC 59.531 52.381 0.00 0.00 0.00 3.95
914 4718 1.821216 GGAGCTGGTGGAATTTCGAA 58.179 50.000 0.00 0.00 0.00 3.71
915 4719 0.391130 CGGAGCTGGTGGAATTTCGA 60.391 55.000 0.00 0.00 0.00 3.71
916 4720 1.369091 CCGGAGCTGGTGGAATTTCG 61.369 60.000 0.00 0.00 0.00 3.46
917 4721 0.035439 TCCGGAGCTGGTGGAATTTC 60.035 55.000 0.00 0.00 0.00 2.17
918 4722 0.035056 CTCCGGAGCTGGTGGAATTT 60.035 55.000 20.67 0.00 0.00 1.82
919 4723 0.909610 TCTCCGGAGCTGGTGGAATT 60.910 55.000 27.39 0.00 0.00 2.17
920 4724 1.306141 TCTCCGGAGCTGGTGGAAT 60.306 57.895 27.39 0.00 0.00 3.01
921 4725 1.984570 CTCTCCGGAGCTGGTGGAA 60.985 63.158 27.39 5.79 32.43 3.53
922 4726 2.363018 CTCTCCGGAGCTGGTGGA 60.363 66.667 27.39 6.88 32.43 4.02
934 4738 4.527583 CTGGCTCCGCAGCTCTCC 62.528 72.222 0.00 0.00 46.03 3.71
935 4739 1.949847 TTACTGGCTCCGCAGCTCTC 61.950 60.000 0.00 0.00 46.03 3.20
936 4740 1.544825 TTTACTGGCTCCGCAGCTCT 61.545 55.000 0.00 0.00 46.03 4.09
937 4741 1.079127 TTTACTGGCTCCGCAGCTC 60.079 57.895 0.00 0.00 46.03 4.09
938 4742 1.376037 GTTTACTGGCTCCGCAGCT 60.376 57.895 0.00 0.00 46.03 4.24
939 4743 1.376037 AGTTTACTGGCTCCGCAGC 60.376 57.895 0.00 0.00 46.06 5.25
940 4744 2.460330 CAGTTTACTGGCTCCGCAG 58.540 57.895 1.88 0.00 40.20 5.18
941 4745 4.693532 CAGTTTACTGGCTCCGCA 57.306 55.556 1.88 0.00 40.20 5.69
949 4753 3.474806 CGGAGCGCCAGTTTACTG 58.525 61.111 7.44 2.86 43.40 2.74
962 4766 6.093495 TGGAGTTATAGTTGAAATTTGCGGAG 59.907 38.462 0.00 0.00 0.00 4.63
963 4767 5.941058 TGGAGTTATAGTTGAAATTTGCGGA 59.059 36.000 0.00 0.00 0.00 5.54
964 4768 6.027749 GTGGAGTTATAGTTGAAATTTGCGG 58.972 40.000 0.00 0.00 0.00 5.69
965 4769 6.027749 GGTGGAGTTATAGTTGAAATTTGCG 58.972 40.000 0.00 0.00 0.00 4.85
966 4770 6.919721 TGGTGGAGTTATAGTTGAAATTTGC 58.080 36.000 0.00 0.00 0.00 3.68
967 4771 7.029563 GCTGGTGGAGTTATAGTTGAAATTTG 58.970 38.462 0.00 0.00 0.00 2.32
968 4772 6.948309 AGCTGGTGGAGTTATAGTTGAAATTT 59.052 34.615 0.00 0.00 0.00 1.82
969 4773 6.485171 AGCTGGTGGAGTTATAGTTGAAATT 58.515 36.000 0.00 0.00 0.00 1.82
970 4774 6.067217 AGCTGGTGGAGTTATAGTTGAAAT 57.933 37.500 0.00 0.00 0.00 2.17
971 4775 5.488341 GAGCTGGTGGAGTTATAGTTGAAA 58.512 41.667 0.00 0.00 0.00 2.69
972 4776 4.081087 GGAGCTGGTGGAGTTATAGTTGAA 60.081 45.833 0.00 0.00 0.00 2.69
973 4777 3.451178 GGAGCTGGTGGAGTTATAGTTGA 59.549 47.826 0.00 0.00 0.00 3.18
974 4778 3.452627 AGGAGCTGGTGGAGTTATAGTTG 59.547 47.826 0.00 0.00 0.00 3.16
975 4779 3.452627 CAGGAGCTGGTGGAGTTATAGTT 59.547 47.826 0.00 0.00 0.00 2.24
976 4780 3.034635 CAGGAGCTGGTGGAGTTATAGT 58.965 50.000 0.00 0.00 0.00 2.12
977 4781 2.366916 CCAGGAGCTGGTGGAGTTATAG 59.633 54.545 5.12 0.00 45.82 1.31
978 4782 2.398588 CCAGGAGCTGGTGGAGTTATA 58.601 52.381 5.12 0.00 45.82 0.98
979 4783 1.207791 CCAGGAGCTGGTGGAGTTAT 58.792 55.000 5.12 0.00 45.82 1.89
980 4784 2.683916 CCAGGAGCTGGTGGAGTTA 58.316 57.895 5.12 0.00 45.82 2.24
981 4785 3.488423 CCAGGAGCTGGTGGAGTT 58.512 61.111 5.12 0.00 45.82 3.01
989 4793 1.380524 CAGCTTCATTCCAGGAGCTG 58.619 55.000 12.07 12.07 42.64 4.24
990 4794 0.990374 ACAGCTTCATTCCAGGAGCT 59.010 50.000 0.00 0.00 0.00 4.09
991 4795 1.093159 CACAGCTTCATTCCAGGAGC 58.907 55.000 0.00 0.00 0.00 4.70
992 4796 1.280133 TCCACAGCTTCATTCCAGGAG 59.720 52.381 0.00 0.00 0.00 3.69
993 4797 1.280133 CTCCACAGCTTCATTCCAGGA 59.720 52.381 0.00 0.00 0.00 3.86
994 4798 1.747709 CTCCACAGCTTCATTCCAGG 58.252 55.000 0.00 0.00 0.00 4.45
995 4799 1.093159 GCTCCACAGCTTCATTCCAG 58.907 55.000 0.00 0.00 43.09 3.86
996 4800 0.674581 CGCTCCACAGCTTCATTCCA 60.675 55.000 0.00 0.00 44.40 3.53
997 4801 0.391661 TCGCTCCACAGCTTCATTCC 60.392 55.000 0.00 0.00 44.40 3.01
998 4802 1.396301 CTTCGCTCCACAGCTTCATTC 59.604 52.381 0.00 0.00 44.40 2.67
999 4803 1.271054 ACTTCGCTCCACAGCTTCATT 60.271 47.619 0.00 0.00 44.40 2.57
1000 4804 0.322975 ACTTCGCTCCACAGCTTCAT 59.677 50.000 0.00 0.00 44.40 2.57
1001 4805 0.966179 TACTTCGCTCCACAGCTTCA 59.034 50.000 0.00 0.00 44.40 3.02
1002 4806 1.351153 GTACTTCGCTCCACAGCTTC 58.649 55.000 0.00 0.00 44.40 3.86
1003 4807 0.037232 GGTACTTCGCTCCACAGCTT 60.037 55.000 0.00 0.00 44.40 3.74
1004 4808 0.900647 AGGTACTTCGCTCCACAGCT 60.901 55.000 0.00 0.00 38.83 4.24
1005 4809 0.458716 GAGGTACTTCGCTCCACAGC 60.459 60.000 0.00 0.00 41.55 4.40
1006 4810 0.173708 GGAGGTACTTCGCTCCACAG 59.826 60.000 10.14 0.00 41.55 3.66
1007 4811 2.273908 GGAGGTACTTCGCTCCACA 58.726 57.895 10.14 0.00 41.55 4.17
1015 4819 0.108281 GCCCTGTTCGGAGGTACTTC 60.108 60.000 0.00 0.00 41.55 3.01
1016 4820 1.551019 GGCCCTGTTCGGAGGTACTT 61.551 60.000 0.00 0.00 41.55 2.24
1018 4822 0.685458 TAGGCCCTGTTCGGAGGTAC 60.685 60.000 0.00 0.00 33.16 3.34
1019 4823 0.263765 ATAGGCCCTGTTCGGAGGTA 59.736 55.000 0.00 0.00 33.16 3.08
1020 4824 0.263765 TATAGGCCCTGTTCGGAGGT 59.736 55.000 0.00 0.00 33.16 3.85
1021 4825 1.645710 ATATAGGCCCTGTTCGGAGG 58.354 55.000 0.00 0.00 33.16 4.30
1022 4826 3.557264 GGAAATATAGGCCCTGTTCGGAG 60.557 52.174 0.00 0.00 33.16 4.63
1023 4827 2.370849 GGAAATATAGGCCCTGTTCGGA 59.629 50.000 0.00 0.00 33.16 4.55
1024 4828 2.552373 GGGAAATATAGGCCCTGTTCGG 60.552 54.545 0.00 0.00 38.85 4.30
1025 4829 2.779506 GGGAAATATAGGCCCTGTTCG 58.220 52.381 0.00 0.00 38.85 3.95
1031 4835 9.226879 AGAGTTTATATAGGGAAATATAGGCCC 57.773 37.037 0.00 0.00 42.37 5.80
1073 4879 0.249031 GTGTGTGCTTTCAGTTGGCC 60.249 55.000 0.00 0.00 0.00 5.36
1081 4887 4.098416 GTCTTGTCTTTGTGTGTGCTTTC 58.902 43.478 0.00 0.00 0.00 2.62
1098 4904 1.060713 CCTCGTGTAGCGTTGTCTTG 58.939 55.000 0.00 0.00 42.13 3.02
1099 4905 0.038526 CCCTCGTGTAGCGTTGTCTT 60.039 55.000 0.00 0.00 42.13 3.01
1100 4906 1.585006 CCCTCGTGTAGCGTTGTCT 59.415 57.895 0.00 0.00 42.13 3.41
1101 4907 2.092882 GCCCTCGTGTAGCGTTGTC 61.093 63.158 0.00 0.00 42.13 3.18
1102 4908 2.048503 GCCCTCGTGTAGCGTTGT 60.049 61.111 0.00 0.00 42.13 3.32
1116 4922 1.040339 TGGCGGAAACCATAATGCCC 61.040 55.000 0.00 0.00 41.77 5.36
1146 4953 2.361357 AGGAGGACGAGGGTGACG 60.361 66.667 0.00 0.00 0.00 4.35
1197 5013 1.069358 GAATCCATCTCTCACCGGACC 59.931 57.143 9.46 0.00 0.00 4.46
1198 5014 2.035632 AGAATCCATCTCTCACCGGAC 58.964 52.381 9.46 0.00 30.46 4.79
1241 5070 2.825836 GGTTCATCCGGCCAGCAG 60.826 66.667 2.24 0.00 0.00 4.24
1519 5352 5.527511 TTTTCGTTACAGTCGACAACAAA 57.472 34.783 19.50 12.60 37.05 2.83
1555 5388 6.084326 AGTTAAATTACACTGCCAAACCAG 57.916 37.500 0.00 0.00 38.78 4.00
1574 5407 9.881529 AAATTTTATTCGAAGCGTGTAAAGTTA 57.118 25.926 3.35 0.00 0.00 2.24
1578 5411 6.520447 CGGAAATTTTATTCGAAGCGTGTAAA 59.480 34.615 3.35 0.33 0.00 2.01
1605 5439 6.698008 TTTATGAGCCTCAACACATTATGG 57.302 37.500 0.00 0.00 0.00 2.74
1617 5451 3.259064 TGTGCGTACTTTTATGAGCCTC 58.741 45.455 4.97 0.00 0.00 4.70
1648 5488 8.240267 AGAGTATCAGGGTACTGTAAAATCTC 57.760 38.462 0.00 0.00 45.14 2.75
1655 5495 6.877855 CGCTTATAGAGTATCAGGGTACTGTA 59.122 42.308 0.00 0.00 45.14 2.74
1657 5497 5.392165 GCGCTTATAGAGTATCAGGGTACTG 60.392 48.000 0.00 0.00 46.30 2.74
1659 5499 4.458295 TGCGCTTATAGAGTATCAGGGTAC 59.542 45.833 9.73 0.00 37.82 3.34
1672 5512 2.096713 GCCGTTGAAGATGCGCTTATAG 60.097 50.000 9.73 0.00 36.83 1.31
1673 5513 1.864711 GCCGTTGAAGATGCGCTTATA 59.135 47.619 9.73 0.00 36.83 0.98
1679 5519 1.154225 GGTTGCCGTTGAAGATGCG 60.154 57.895 0.00 0.00 0.00 4.73
1710 5551 3.198635 CCTTATCCATGGATAGATGCGGT 59.801 47.826 28.89 9.01 38.21 5.68
1718 5559 2.546899 CGGTCCCCTTATCCATGGATA 58.453 52.381 27.46 27.46 36.17 2.59
1724 5567 1.383525 GGACCGGTCCCCTTATCCA 60.384 63.158 39.24 0.00 43.94 3.41
1738 5582 4.699522 GTCCTGTGCCCGTGGACC 62.700 72.222 0.00 0.00 43.10 4.46
1750 5594 4.436998 GTGTCCTCCCGCGTCCTG 62.437 72.222 4.92 0.00 0.00 3.86
1755 5599 4.530857 GGATGGTGTCCTCCCGCG 62.531 72.222 0.00 0.00 44.16 6.46
1959 5811 5.095145 AGTCTAGTGTAGTCCGTGTCATA 57.905 43.478 0.00 0.00 0.00 2.15
1970 5822 4.057432 GGCCGTAGACTAGTCTAGTGTAG 58.943 52.174 29.00 17.55 42.31 2.74
1971 5823 3.491619 CGGCCGTAGACTAGTCTAGTGTA 60.492 52.174 29.00 14.37 42.31 2.90
1973 5825 1.865970 CGGCCGTAGACTAGTCTAGTG 59.134 57.143 29.00 23.26 42.31 2.74
1975 5827 1.510776 CCGGCCGTAGACTAGTCTAG 58.489 60.000 29.00 20.22 42.31 2.43
1976 5828 0.533755 GCCGGCCGTAGACTAGTCTA 60.534 60.000 25.58 25.58 40.93 2.59
1977 5829 1.823041 GCCGGCCGTAGACTAGTCT 60.823 63.158 27.72 27.72 43.40 3.24
1997 5850 1.961180 AAGACGAAGGGATCCGCCAG 61.961 60.000 5.45 0.00 38.95 4.85
2011 5864 2.106683 GCCGGACATGGGAAAGACG 61.107 63.158 5.05 0.00 0.00 4.18
2030 5883 1.597797 CGTAGTCCGGTTAGTGGGCA 61.598 60.000 0.00 0.00 31.97 5.36
2049 5904 5.297569 AGAATATGCTTACAAGACTCCCC 57.702 43.478 0.00 0.00 0.00 4.81
2057 5912 7.985184 AGATACGGTGAAAGAATATGCTTACAA 59.015 33.333 0.00 0.00 0.00 2.41
2060 5915 7.656137 GGAAGATACGGTGAAAGAATATGCTTA 59.344 37.037 0.00 0.00 0.00 3.09
2062 5917 5.992217 GGAAGATACGGTGAAAGAATATGCT 59.008 40.000 0.00 0.00 0.00 3.79
2075 5930 2.236766 CGGACATAGGGAAGATACGGT 58.763 52.381 0.00 0.00 0.00 4.83
2111 5966 0.990374 AGCATCCTCTTTGCCACTCT 59.010 50.000 0.00 0.00 41.06 3.24
2160 6018 1.074775 GTTGGCACACCCATCTGGA 59.925 57.895 0.00 0.00 44.89 3.86
2212 6070 1.372997 CGTCGCCAGCTTGTACAGT 60.373 57.895 0.00 0.00 0.00 3.55
2269 6127 1.135053 GGAGAAGTAGAACACGGGAGC 60.135 57.143 0.00 0.00 0.00 4.70
2323 6181 1.728069 CGGATGTCGACGAGGTGAT 59.272 57.895 11.62 0.00 42.43 3.06
2382 6240 1.227350 CATCCTCCTTCGATGCGCA 60.227 57.895 14.96 14.96 31.37 6.09


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

AutoCloner maintained by Alex Coulton.