Multiple sequence alignment - TraesCS7A01G042500

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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 TraesCS7A01G042500 chr7A 100.000 2528 0 0 1 2528 19815393 19817920 0.000000e+00 4669
1 TraesCS7A01G042500 chr7A 95.506 623 27 1 1 623 1428984 1429605 0.000000e+00 994
2 TraesCS7A01G042500 chr7A 94.569 626 31 3 1 623 5011164 5011789 0.000000e+00 965
3 TraesCS7A01G042500 chr7A 81.875 320 45 7 1223 1529 32528856 32529175 8.970000e-65 257
4 TraesCS7A01G042500 chr7A 85.306 245 32 4 1262 1504 12283496 12283254 1.500000e-62 250
5 TraesCS7A01G042500 chr7A 86.026 229 30 2 1277 1504 12198354 12198127 6.990000e-61 244
6 TraesCS7A01G042500 chr7A 85.281 231 34 0 1277 1507 12202283 12202053 3.250000e-59 239
7 TraesCS7A01G042500 chr7D 88.902 1721 122 27 832 2528 19391357 19393032 0.000000e+00 2056
8 TraesCS7A01G042500 chr7D 82.769 325 42 8 1222 1535 32330276 32330597 6.890000e-71 278
9 TraesCS7A01G042500 chr7D 87.773 229 26 2 1277 1504 12546861 12546634 1.490000e-67 267
10 TraesCS7A01G042500 chr4A 90.676 858 58 11 700 1557 713631295 713630460 0.000000e+00 1122
11 TraesCS7A01G042500 chr4A 95.477 619 27 1 5 623 36395800 36395183 0.000000e+00 987
12 TraesCS7A01G042500 chr4A 82.696 601 67 21 1642 2237 713630408 713629840 1.350000e-137 499
13 TraesCS7A01G042500 chr4A 85.656 244 33 2 1262 1504 725581460 725581702 3.230000e-64 255
14 TraesCS7A01G042500 chr5A 97.753 623 14 0 1 623 668166472 668165850 0.000000e+00 1074
15 TraesCS7A01G042500 chr1A 96.469 623 21 1 1 623 3436365 3436986 0.000000e+00 1027
16 TraesCS7A01G042500 chr6A 95.833 624 23 3 1 623 615705388 615704767 0.000000e+00 1005
17 TraesCS7A01G042500 chr3A 95.666 623 26 1 1 623 576673700 576673079 0.000000e+00 1000
18 TraesCS7A01G042500 chr2A 95.506 623 27 1 1 623 750196135 750196756 0.000000e+00 994
19 TraesCS7A01G042500 chr2A 94.695 622 32 1 1 622 778640853 778640233 0.000000e+00 965


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 TraesCS7A01G042500 chr7A 19815393 19817920 2527 False 4669.0 4669 100.0000 1 2528 1 chr7A.!!$F3 2527
1 TraesCS7A01G042500 chr7A 1428984 1429605 621 False 994.0 994 95.5060 1 623 1 chr7A.!!$F1 622
2 TraesCS7A01G042500 chr7A 5011164 5011789 625 False 965.0 965 94.5690 1 623 1 chr7A.!!$F2 622
3 TraesCS7A01G042500 chr7A 12198127 12202283 4156 True 241.5 244 85.6535 1277 1507 2 chr7A.!!$R2 230
4 TraesCS7A01G042500 chr7D 19391357 19393032 1675 False 2056.0 2056 88.9020 832 2528 1 chr7D.!!$F1 1696
5 TraesCS7A01G042500 chr4A 36395183 36395800 617 True 987.0 987 95.4770 5 623 1 chr4A.!!$R1 618
6 TraesCS7A01G042500 chr4A 713629840 713631295 1455 True 810.5 1122 86.6860 700 2237 2 chr4A.!!$R2 1537
7 TraesCS7A01G042500 chr5A 668165850 668166472 622 True 1074.0 1074 97.7530 1 623 1 chr5A.!!$R1 622
8 TraesCS7A01G042500 chr1A 3436365 3436986 621 False 1027.0 1027 96.4690 1 623 1 chr1A.!!$F1 622
9 TraesCS7A01G042500 chr6A 615704767 615705388 621 True 1005.0 1005 95.8330 1 623 1 chr6A.!!$R1 622
10 TraesCS7A01G042500 chr3A 576673079 576673700 621 True 1000.0 1000 95.6660 1 623 1 chr3A.!!$R1 622
11 TraesCS7A01G042500 chr2A 750196135 750196756 621 False 994.0 994 95.5060 1 623 1 chr2A.!!$F1 622
12 TraesCS7A01G042500 chr2A 778640233 778640853 620 True 965.0 965 94.6950 1 622 1 chr2A.!!$R1 621

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
603 608 0.038166 ATTCAAAGCCGGGCTCTTCA 59.962 50.0 24.08 7.71 38.25 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1618 5101 0.038599 TGGATGCATGACTGGCAAGT 59.961 50.0 2.46 0.0 45.6 3.16 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
47 48 3.240134 GACCTTGCTGGAGGCGTCA 62.240 63.158 8.91 0.00 45.43 4.35
511 515 3.136626 AGTGAGTAGGCTTTCCAGTGTTT 59.863 43.478 0.00 0.00 33.74 2.83
603 608 0.038166 ATTCAAAGCCGGGCTCTTCA 59.962 50.000 24.08 7.71 38.25 3.02
607 612 2.185310 AAAGCCGGGCTCTTCACGAT 62.185 55.000 24.08 0.00 38.25 3.73
643 648 3.141409 TTTTTCAGGGGTGGGCTTC 57.859 52.632 0.00 0.00 0.00 3.86
644 649 0.263172 TTTTTCAGGGGTGGGCTTCA 59.737 50.000 0.00 0.00 0.00 3.02
645 650 0.178964 TTTTCAGGGGTGGGCTTCAG 60.179 55.000 0.00 0.00 0.00 3.02
646 651 1.065410 TTTCAGGGGTGGGCTTCAGA 61.065 55.000 0.00 0.00 0.00 3.27
647 652 0.846427 TTCAGGGGTGGGCTTCAGAT 60.846 55.000 0.00 0.00 0.00 2.90
648 653 0.846427 TCAGGGGTGGGCTTCAGATT 60.846 55.000 0.00 0.00 0.00 2.40
649 654 0.682209 CAGGGGTGGGCTTCAGATTG 60.682 60.000 0.00 0.00 0.00 2.67
650 655 1.142688 AGGGGTGGGCTTCAGATTGT 61.143 55.000 0.00 0.00 0.00 2.71
651 656 0.623723 GGGGTGGGCTTCAGATTGTA 59.376 55.000 0.00 0.00 0.00 2.41
652 657 1.005450 GGGGTGGGCTTCAGATTGTAA 59.995 52.381 0.00 0.00 0.00 2.41
653 658 2.358195 GGGGTGGGCTTCAGATTGTAAT 60.358 50.000 0.00 0.00 0.00 1.89
654 659 3.365472 GGGTGGGCTTCAGATTGTAATT 58.635 45.455 0.00 0.00 0.00 1.40
655 660 3.131046 GGGTGGGCTTCAGATTGTAATTG 59.869 47.826 0.00 0.00 0.00 2.32
656 661 3.763897 GGTGGGCTTCAGATTGTAATTGT 59.236 43.478 0.00 0.00 0.00 2.71
657 662 4.380867 GGTGGGCTTCAGATTGTAATTGTG 60.381 45.833 0.00 0.00 0.00 3.33
658 663 3.193267 TGGGCTTCAGATTGTAATTGTGC 59.807 43.478 0.00 0.00 0.00 4.57
659 664 3.193267 GGGCTTCAGATTGTAATTGTGCA 59.807 43.478 0.00 0.00 0.00 4.57
660 665 4.168760 GGCTTCAGATTGTAATTGTGCAC 58.831 43.478 10.75 10.75 0.00 4.57
661 666 4.321156 GGCTTCAGATTGTAATTGTGCACA 60.321 41.667 17.42 17.42 0.00 4.57
662 667 5.404946 GCTTCAGATTGTAATTGTGCACAT 58.595 37.500 22.39 9.53 0.00 3.21
663 668 5.287752 GCTTCAGATTGTAATTGTGCACATG 59.712 40.000 22.39 12.55 0.00 3.21
664 669 4.735985 TCAGATTGTAATTGTGCACATGC 58.264 39.130 22.39 11.07 42.50 4.06
665 670 3.544682 CAGATTGTAATTGTGCACATGCG 59.455 43.478 22.39 0.00 45.83 4.73
666 671 3.191162 AGATTGTAATTGTGCACATGCGT 59.809 39.130 22.39 8.74 45.83 5.24
667 672 2.328655 TGTAATTGTGCACATGCGTG 57.671 45.000 22.39 3.82 46.56 5.34
668 673 1.606189 TGTAATTGTGCACATGCGTGT 59.394 42.857 22.39 5.51 45.50 4.49
669 674 2.808543 TGTAATTGTGCACATGCGTGTA 59.191 40.909 22.39 3.59 45.50 2.90
670 675 3.438434 TGTAATTGTGCACATGCGTGTAT 59.562 39.130 22.39 6.21 45.50 2.29
671 676 2.547913 ATTGTGCACATGCGTGTATG 57.452 45.000 22.39 1.29 45.50 2.39
672 677 0.109827 TTGTGCACATGCGTGTATGC 60.110 50.000 22.39 12.74 45.50 3.14
673 678 0.954938 TGTGCACATGCGTGTATGCT 60.955 50.000 17.42 0.00 45.50 3.79
674 679 0.247814 GTGCACATGCGTGTATGCTC 60.248 55.000 18.91 13.30 45.50 4.26
675 680 1.011904 GCACATGCGTGTATGCTCG 60.012 57.895 12.10 0.00 45.50 5.03
676 681 1.637934 CACATGCGTGTATGCTCGG 59.362 57.895 12.10 0.00 38.41 4.63
677 682 1.083806 CACATGCGTGTATGCTCGGT 61.084 55.000 12.10 0.00 38.41 4.69
678 683 0.806102 ACATGCGTGTATGCTCGGTC 60.806 55.000 10.57 0.00 36.63 4.79
679 684 0.805711 CATGCGTGTATGCTCGGTCA 60.806 55.000 7.36 0.00 35.36 4.02
680 685 0.108377 ATGCGTGTATGCTCGGTCAA 60.108 50.000 7.36 0.00 35.36 3.18
681 686 0.319986 TGCGTGTATGCTCGGTCAAA 60.320 50.000 7.36 0.00 35.36 2.69
682 687 0.793861 GCGTGTATGCTCGGTCAAAA 59.206 50.000 7.36 0.00 32.87 2.44
683 688 1.195900 GCGTGTATGCTCGGTCAAAAA 59.804 47.619 7.36 0.00 32.87 1.94
684 689 2.159572 GCGTGTATGCTCGGTCAAAAAT 60.160 45.455 7.36 0.00 32.87 1.82
685 690 3.062909 GCGTGTATGCTCGGTCAAAAATA 59.937 43.478 7.36 0.00 32.87 1.40
686 691 4.260620 GCGTGTATGCTCGGTCAAAAATAT 60.261 41.667 7.36 0.00 32.87 1.28
687 692 5.197549 CGTGTATGCTCGGTCAAAAATATG 58.802 41.667 0.00 0.00 0.00 1.78
688 693 5.220586 CGTGTATGCTCGGTCAAAAATATGT 60.221 40.000 0.00 0.00 0.00 2.29
689 694 5.965334 GTGTATGCTCGGTCAAAAATATGTG 59.035 40.000 0.00 0.00 0.00 3.21
690 695 5.645929 TGTATGCTCGGTCAAAAATATGTGT 59.354 36.000 0.00 0.00 0.00 3.72
691 696 4.678509 TGCTCGGTCAAAAATATGTGTC 57.321 40.909 0.00 0.00 0.00 3.67
692 697 4.323417 TGCTCGGTCAAAAATATGTGTCT 58.677 39.130 0.00 0.00 0.00 3.41
693 698 4.759693 TGCTCGGTCAAAAATATGTGTCTT 59.240 37.500 0.00 0.00 0.00 3.01
694 699 5.935206 TGCTCGGTCAAAAATATGTGTCTTA 59.065 36.000 0.00 0.00 0.00 2.10
695 700 6.092122 TGCTCGGTCAAAAATATGTGTCTTAG 59.908 38.462 0.00 0.00 0.00 2.18
696 701 6.092259 GCTCGGTCAAAAATATGTGTCTTAGT 59.908 38.462 0.00 0.00 0.00 2.24
697 702 7.359262 TCGGTCAAAAATATGTGTCTTAGTG 57.641 36.000 0.00 0.00 0.00 2.74
698 703 7.156000 TCGGTCAAAAATATGTGTCTTAGTGA 58.844 34.615 0.00 0.00 0.00 3.41
733 738 5.890424 TTTTCAAGGACGTTGAGAAAAGT 57.110 34.783 10.42 0.00 46.09 2.66
747 752 4.828939 TGAGAAAAGTAGTACGTTCTCCCA 59.171 41.667 28.54 18.35 40.40 4.37
749 754 3.565905 AAAGTAGTACGTTCTCCCACG 57.434 47.619 0.00 0.00 46.04 4.94
754 759 5.128919 AGTAGTACGTTCTCCCACGATTAT 58.871 41.667 0.00 0.00 43.15 1.28
761 766 2.019249 TCTCCCACGATTATCGACGTT 58.981 47.619 21.93 0.00 43.74 3.99
765 770 2.286359 CCCACGATTATCGACGTTCGTA 60.286 50.000 21.93 0.00 43.74 3.43
766 771 2.710961 CCACGATTATCGACGTTCGTAC 59.289 50.000 21.93 0.00 43.74 3.67
770 775 2.178474 TTATCGACGTTCGTACAGGC 57.822 50.000 0.00 0.00 41.35 4.85
772 777 0.455633 ATCGACGTTCGTACAGGCAC 60.456 55.000 0.00 0.00 41.35 5.01
780 785 3.581755 GTTCGTACAGGCACTTGATGTA 58.418 45.455 0.00 0.00 34.60 2.29
781 786 3.503827 TCGTACAGGCACTTGATGTAG 57.496 47.619 0.00 0.00 34.60 2.74
785 790 3.769739 ACAGGCACTTGATGTAGTGAA 57.230 42.857 7.88 0.00 46.72 3.18
789 794 6.237901 ACAGGCACTTGATGTAGTGAATTTA 58.762 36.000 7.88 0.00 46.72 1.40
793 798 6.907212 GGCACTTGATGTAGTGAATTTATTCG 59.093 38.462 7.88 0.00 46.72 3.34
798 803 9.490663 CTTGATGTAGTGAATTTATTCGGAAAC 57.509 33.333 0.00 0.00 39.62 2.78
801 806 8.786826 ATGTAGTGAATTTATTCGGAAACTCA 57.213 30.769 0.00 0.00 39.62 3.41
809 814 2.417339 TTCGGAAACTCAGTGACTCG 57.583 50.000 0.00 0.00 0.00 4.18
811 816 1.535896 TCGGAAACTCAGTGACTCGAG 59.464 52.381 11.84 11.84 35.30 4.04
814 819 2.351932 GGAAACTCAGTGACTCGAGTCC 60.352 54.545 36.01 27.51 41.60 3.85
817 822 1.091537 CTCAGTGACTCGAGTCCTCC 58.908 60.000 36.01 25.07 44.15 4.30
819 824 0.673956 CAGTGACTCGAGTCCTCCGA 60.674 60.000 36.01 19.03 44.15 4.55
852 857 4.507756 GCGAGTATATGTGAAGTGCATTCA 59.492 41.667 7.27 7.27 45.79 2.57
869 876 4.449068 GCATTCATGTGTCCGTATAGAAGG 59.551 45.833 0.00 0.00 0.00 3.46
928 937 8.791355 AAAGAACGTGACAAAAATAATACACC 57.209 30.769 0.00 0.00 0.00 4.16
967 976 1.872773 TTTTCCCTTTTGCAGGTGGT 58.127 45.000 0.00 0.00 42.02 4.16
987 996 0.737367 CGACATGAGATGCACCGTGT 60.737 55.000 0.00 9.38 35.44 4.49
1028 1037 1.998315 CTCTATACATGCAGCGATGGC 59.002 52.381 1.46 0.00 40.37 4.40
1030 1039 0.316841 TATACATGCAGCGATGGCGA 59.683 50.000 1.46 0.00 46.35 5.54
1031 1040 0.321034 ATACATGCAGCGATGGCGAT 60.321 50.000 1.46 0.00 46.35 4.58
1061 1070 1.753848 GCACATGGCCACCAGCATA 60.754 57.895 8.16 0.00 46.50 3.14
1062 1071 2.008268 GCACATGGCCACCAGCATAC 62.008 60.000 8.16 0.00 46.50 2.39
1160 1169 0.033504 CACCGCTCCGCCTACATAAT 59.966 55.000 0.00 0.00 0.00 1.28
1201 1210 1.475213 CGGGGATAAGAAGGGAAGCAC 60.475 57.143 0.00 0.00 0.00 4.40
1203 1212 1.485066 GGGATAAGAAGGGAAGCACGA 59.515 52.381 0.00 0.00 0.00 4.35
1204 1213 2.093128 GGGATAAGAAGGGAAGCACGAA 60.093 50.000 0.00 0.00 0.00 3.85
1205 1214 3.198872 GGATAAGAAGGGAAGCACGAAG 58.801 50.000 0.00 0.00 0.00 3.79
1206 1215 2.094762 TAAGAAGGGAAGCACGAAGC 57.905 50.000 0.00 0.00 46.19 3.86
1217 1226 2.024176 GCACGAAGCAACAAGAAGAC 57.976 50.000 0.00 0.00 44.79 3.01
1221 1230 1.136884 CGAAGCAACAAGAAGACGACG 60.137 52.381 0.00 0.00 0.00 5.12
1238 1247 0.952984 ACGAAGAAGAAGCAGCAGCC 60.953 55.000 0.00 0.00 43.56 4.85
1602 5085 2.358125 TTGCCTGCACGTGCGTAT 60.358 55.556 33.22 0.00 45.83 3.06
1618 5101 2.731027 GCGTATGTCGTGTGTGATCTGA 60.731 50.000 0.00 0.00 42.13 3.27
1627 5110 1.417517 TGTGTGATCTGACTTGCCAGT 59.582 47.619 0.00 0.00 35.71 4.00
1713 5197 2.411676 CGTTCGTGTTTGTGTTGTGTCA 60.412 45.455 0.00 0.00 0.00 3.58
1818 5305 5.009610 TGTTTCCTTTCCTCTGTTTATGTGC 59.990 40.000 0.00 0.00 0.00 4.57
1863 5358 6.777091 TCAGAGGGACAAAATTCTGAAAATCA 59.223 34.615 0.00 0.00 42.08 2.57
1905 5402 9.249457 TGTTCTTGATCTATAAAAGCATCTACG 57.751 33.333 0.00 0.00 0.00 3.51
1906 5408 8.704234 GTTCTTGATCTATAAAAGCATCTACGG 58.296 37.037 0.00 0.00 0.00 4.02
1946 5448 1.154225 CAAACGTCCAGCGGCATTC 60.154 57.895 1.45 0.00 46.52 2.67
1948 5450 4.778143 ACGTCCAGCGGCATTCCC 62.778 66.667 1.45 0.00 46.52 3.97
1959 5461 1.739667 GCATTCCCGGTTATTGCCC 59.260 57.895 0.00 0.00 0.00 5.36
1960 5462 1.040339 GCATTCCCGGTTATTGCCCA 61.040 55.000 0.00 0.00 0.00 5.36
1965 5467 1.697432 TCCCGGTTATTGCCCAGATAG 59.303 52.381 0.00 0.00 0.00 2.08
1994 5496 1.982958 ACCCAACCGGACTAGACAAAT 59.017 47.619 9.46 0.00 34.64 2.32
2020 5523 2.036992 TCCAAACGTTTAGCCTAACCGA 59.963 45.455 14.20 0.00 0.00 4.69
2032 5535 2.805845 CCTAACCGACAACCTCATACG 58.194 52.381 0.00 0.00 0.00 3.06
2053 5556 2.291411 GCAGCCCATATCTGGAATGGAT 60.291 50.000 0.00 0.00 45.77 3.41
2057 5560 3.887716 GCCCATATCTGGAATGGATATGC 59.112 47.826 14.57 4.93 45.77 3.14
2058 5561 4.629449 GCCCATATCTGGAATGGATATGCA 60.629 45.833 14.57 0.00 45.77 3.96
2065 5568 2.224843 TGGAATGGATATGCAGCGGATT 60.225 45.455 2.55 0.00 0.00 3.01
2077 5580 3.661911 CGGATTTGACGCACCCAA 58.338 55.556 0.00 0.00 0.00 4.12
2090 5593 4.569180 CCCAATCGCCGCCTCCAT 62.569 66.667 0.00 0.00 0.00 3.41
2134 5637 0.405585 CCTCACCTTTGTCCCCACAT 59.594 55.000 0.00 0.00 30.55 3.21
2176 5679 2.650322 ACCCTCACTCTCTTGACCTCTA 59.350 50.000 0.00 0.00 0.00 2.43
2182 5685 2.088423 CTCTCTTGACCTCTACGCTGT 58.912 52.381 0.00 0.00 0.00 4.40
2229 5732 2.819595 CCTCCACAATGGTCGGCG 60.820 66.667 0.00 0.00 39.03 6.46
2231 5734 1.153369 CTCCACAATGGTCGGCGAT 60.153 57.895 14.79 0.00 39.03 4.58
2237 5740 0.588252 CAATGGTCGGCGATGGATTC 59.412 55.000 14.79 0.00 0.00 2.52
2268 5771 1.080093 GACGTGATCGACTGGGCAA 60.080 57.895 0.00 0.00 40.62 4.52
2269 5772 1.352156 GACGTGATCGACTGGGCAAC 61.352 60.000 0.00 0.00 40.62 4.17
2288 5791 2.363018 CTCGCCAGGGAGGACTCA 60.363 66.667 3.89 0.00 41.22 3.41
2297 5800 1.008206 AGGGAGGACTCAAGCTCATCT 59.992 52.381 1.32 0.00 0.00 2.90
2309 5812 3.876274 AGCTCATCTGTGTTGTACGAT 57.124 42.857 0.00 0.00 0.00 3.73
2319 5822 2.094700 GTGTTGTACGATGAGGAGCTCA 60.095 50.000 17.19 0.00 44.99 4.26
2344 5847 2.413142 GCATTGCCCTCTGCCACTC 61.413 63.158 0.00 0.00 40.16 3.51
2382 5888 4.719369 GCTCCTCGACGGCGTTGT 62.719 66.667 25.32 0.00 38.98 3.32
2384 5890 3.263503 CTCCTCGACGGCGTTGTCA 62.264 63.158 25.32 7.79 38.84 3.58
2396 5902 1.754745 GTTGTCAGTGGCCCAGAGA 59.245 57.895 0.00 0.00 0.00 3.10
2397 5903 0.321122 GTTGTCAGTGGCCCAGAGAG 60.321 60.000 0.00 0.00 0.00 3.20
2410 5916 0.380378 CAGAGAGGCAGTCGTAGCTC 59.620 60.000 0.00 0.00 0.00 4.09
2412 5918 1.487142 AGAGAGGCAGTCGTAGCTCTA 59.513 52.381 0.00 0.00 31.49 2.43
2447 5953 4.373116 ATGACGTGGTCCGCGCTT 62.373 61.111 24.45 12.22 41.33 4.68
2461 5967 1.766143 GCGCTTGATTAGACGGCAGG 61.766 60.000 0.00 0.00 0.00 4.85
2504 6010 1.078848 CAGCCCCTTCTCCTTGACG 60.079 63.158 0.00 0.00 0.00 4.35
2508 6014 1.296715 CCCTTCTCCTTGACGGTGG 59.703 63.158 0.00 0.00 32.70 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 64 2.588034 GCATAACCTCCCGACCGC 60.588 66.667 0.00 0.00 0.00 5.68
299 301 0.473117 TCACCGAAGAGGGACCCTTT 60.473 55.000 16.22 6.00 46.96 3.11
511 515 1.203052 GGTCAGAACGATACAACGGGA 59.797 52.381 0.00 0.00 37.61 5.14
625 630 0.263172 TGAAGCCCACCCCTGAAAAA 59.737 50.000 0.00 0.00 0.00 1.94
626 631 0.178964 CTGAAGCCCACCCCTGAAAA 60.179 55.000 0.00 0.00 0.00 2.29
627 632 1.065410 TCTGAAGCCCACCCCTGAAA 61.065 55.000 0.00 0.00 0.00 2.69
628 633 0.846427 ATCTGAAGCCCACCCCTGAA 60.846 55.000 0.00 0.00 0.00 3.02
629 634 0.846427 AATCTGAAGCCCACCCCTGA 60.846 55.000 0.00 0.00 0.00 3.86
630 635 0.682209 CAATCTGAAGCCCACCCCTG 60.682 60.000 0.00 0.00 0.00 4.45
631 636 1.142688 ACAATCTGAAGCCCACCCCT 61.143 55.000 0.00 0.00 0.00 4.79
632 637 0.623723 TACAATCTGAAGCCCACCCC 59.376 55.000 0.00 0.00 0.00 4.95
633 638 2.507407 TTACAATCTGAAGCCCACCC 57.493 50.000 0.00 0.00 0.00 4.61
634 639 3.763897 ACAATTACAATCTGAAGCCCACC 59.236 43.478 0.00 0.00 0.00 4.61
635 640 4.737054 CACAATTACAATCTGAAGCCCAC 58.263 43.478 0.00 0.00 0.00 4.61
636 641 3.193267 GCACAATTACAATCTGAAGCCCA 59.807 43.478 0.00 0.00 0.00 5.36
637 642 3.193267 TGCACAATTACAATCTGAAGCCC 59.807 43.478 0.00 0.00 0.00 5.19
638 643 4.168760 GTGCACAATTACAATCTGAAGCC 58.831 43.478 13.17 0.00 0.00 4.35
639 644 4.797471 TGTGCACAATTACAATCTGAAGC 58.203 39.130 19.28 0.00 0.00 3.86
640 645 5.287752 GCATGTGCACAATTACAATCTGAAG 59.712 40.000 25.72 0.00 41.59 3.02
641 646 5.162794 GCATGTGCACAATTACAATCTGAA 58.837 37.500 25.72 0.00 41.59 3.02
642 647 4.672283 CGCATGTGCACAATTACAATCTGA 60.672 41.667 25.72 0.00 42.21 3.27
643 648 3.544682 CGCATGTGCACAATTACAATCTG 59.455 43.478 25.72 14.93 42.21 2.90
644 649 3.191162 ACGCATGTGCACAATTACAATCT 59.809 39.130 25.72 0.00 42.21 2.40
645 650 3.301379 CACGCATGTGCACAATTACAATC 59.699 43.478 25.72 5.87 39.67 2.67
646 651 3.244156 CACGCATGTGCACAATTACAAT 58.756 40.909 25.72 1.57 39.67 2.71
647 652 2.659387 CACGCATGTGCACAATTACAA 58.341 42.857 25.72 0.00 39.67 2.41
648 653 2.328655 CACGCATGTGCACAATTACA 57.671 45.000 25.72 0.00 39.67 2.41
659 664 0.806102 GACCGAGCATACACGCATGT 60.806 55.000 0.00 0.00 43.30 3.21
660 665 0.805711 TGACCGAGCATACACGCATG 60.806 55.000 0.00 0.00 0.00 4.06
661 666 0.108377 TTGACCGAGCATACACGCAT 60.108 50.000 0.00 0.00 0.00 4.73
662 667 0.319986 TTTGACCGAGCATACACGCA 60.320 50.000 0.00 0.00 0.00 5.24
663 668 0.793861 TTTTGACCGAGCATACACGC 59.206 50.000 0.00 0.00 0.00 5.34
664 669 3.740044 ATTTTTGACCGAGCATACACG 57.260 42.857 0.00 0.00 0.00 4.49
665 670 5.965334 CACATATTTTTGACCGAGCATACAC 59.035 40.000 0.00 0.00 0.00 2.90
666 671 5.645929 ACACATATTTTTGACCGAGCATACA 59.354 36.000 0.00 0.00 0.00 2.29
667 672 6.037172 AGACACATATTTTTGACCGAGCATAC 59.963 38.462 0.00 0.00 0.00 2.39
668 673 6.112734 AGACACATATTTTTGACCGAGCATA 58.887 36.000 0.00 0.00 0.00 3.14
669 674 4.943705 AGACACATATTTTTGACCGAGCAT 59.056 37.500 0.00 0.00 0.00 3.79
670 675 4.323417 AGACACATATTTTTGACCGAGCA 58.677 39.130 0.00 0.00 0.00 4.26
671 676 4.946784 AGACACATATTTTTGACCGAGC 57.053 40.909 0.00 0.00 0.00 5.03
672 677 7.330946 TCACTAAGACACATATTTTTGACCGAG 59.669 37.037 0.00 0.00 0.00 4.63
673 678 7.156000 TCACTAAGACACATATTTTTGACCGA 58.844 34.615 0.00 0.00 0.00 4.69
674 679 7.359262 TCACTAAGACACATATTTTTGACCG 57.641 36.000 0.00 0.00 0.00 4.79
675 680 8.784043 ACTTCACTAAGACACATATTTTTGACC 58.216 33.333 0.00 0.00 36.50 4.02
680 685 9.998106 ACTGTACTTCACTAAGACACATATTTT 57.002 29.630 0.00 0.00 36.50 1.82
685 690 9.998106 AAAATACTGTACTTCACTAAGACACAT 57.002 29.630 0.00 0.00 36.50 3.21
686 691 9.826574 AAAAATACTGTACTTCACTAAGACACA 57.173 29.630 0.00 0.00 36.50 3.72
714 719 5.272283 ACTACTTTTCTCAACGTCCTTGA 57.728 39.130 0.00 0.00 36.46 3.02
715 720 5.116680 CGTACTACTTTTCTCAACGTCCTTG 59.883 44.000 0.00 0.00 0.00 3.61
718 723 4.540824 ACGTACTACTTTTCTCAACGTCC 58.459 43.478 0.00 0.00 37.53 4.79
722 727 5.632764 GGGAGAACGTACTACTTTTCTCAAC 59.367 44.000 19.46 12.68 43.88 3.18
728 733 3.569701 TCGTGGGAGAACGTACTACTTTT 59.430 43.478 0.00 0.00 43.96 2.27
731 736 2.479566 TCGTGGGAGAACGTACTACT 57.520 50.000 0.00 0.00 43.96 2.57
732 737 3.772060 AATCGTGGGAGAACGTACTAC 57.228 47.619 0.00 0.00 43.96 2.73
733 738 4.212004 CGATAATCGTGGGAGAACGTACTA 59.788 45.833 0.00 0.00 43.96 1.82
749 754 2.718027 GCCTGTACGAACGTCGATAATC 59.282 50.000 13.06 0.00 43.74 1.75
754 759 1.081906 GTGCCTGTACGAACGTCGA 60.082 57.895 13.06 0.00 43.74 4.20
761 766 2.823747 ACTACATCAAGTGCCTGTACGA 59.176 45.455 0.00 0.00 0.00 3.43
765 770 3.769739 TTCACTACATCAAGTGCCTGT 57.230 42.857 0.00 0.00 45.34 4.00
766 771 5.633830 AAATTCACTACATCAAGTGCCTG 57.366 39.130 0.00 0.00 45.34 4.85
770 775 8.196802 TCCGAATAAATTCACTACATCAAGTG 57.803 34.615 3.76 0.00 46.78 3.16
772 777 9.490663 GTTTCCGAATAAATTCACTACATCAAG 57.509 33.333 3.76 0.00 36.61 3.02
780 785 6.934645 TCACTGAGTTTCCGAATAAATTCACT 59.065 34.615 3.76 0.00 36.61 3.41
781 786 7.015877 GTCACTGAGTTTCCGAATAAATTCAC 58.984 38.462 3.76 0.00 36.61 3.18
785 790 5.577164 CGAGTCACTGAGTTTCCGAATAAAT 59.423 40.000 0.00 0.00 0.00 1.40
789 794 2.557056 TCGAGTCACTGAGTTTCCGAAT 59.443 45.455 0.00 0.00 0.00 3.34
793 798 2.351932 GGACTCGAGTCACTGAGTTTCC 60.352 54.545 38.52 19.74 45.09 3.13
798 803 1.091537 GGAGGACTCGAGTCACTGAG 58.908 60.000 38.52 5.18 46.47 3.35
801 806 0.391927 CTCGGAGGACTCGAGTCACT 60.392 60.000 38.52 32.15 46.16 3.41
809 814 1.096416 ACATCGTTCTCGGAGGACTC 58.904 55.000 14.31 0.00 37.69 3.36
811 816 0.802607 GCACATCGTTCTCGGAGGAC 60.803 60.000 6.35 6.35 37.69 3.85
814 819 0.863538 CTCGCACATCGTTCTCGGAG 60.864 60.000 0.00 0.00 39.67 4.63
817 822 2.106750 ATACTCGCACATCGTTCTCG 57.893 50.000 0.00 0.00 39.67 4.04
819 824 4.036380 TCACATATACTCGCACATCGTTCT 59.964 41.667 0.00 0.00 39.67 3.01
852 857 6.370718 GTGTTTTTCCTTCTATACGGACACAT 59.629 38.462 0.00 0.00 0.00 3.21
853 858 5.697633 GTGTTTTTCCTTCTATACGGACACA 59.302 40.000 0.00 0.00 0.00 3.72
854 859 5.164022 CGTGTTTTTCCTTCTATACGGACAC 60.164 44.000 0.00 0.00 0.00 3.67
869 876 8.288217 TCTTGGTTTTAATATGCGTGTTTTTC 57.712 30.769 0.00 0.00 0.00 2.29
922 931 2.093128 GGATTTCCCACACTCGGTGTAT 60.093 50.000 8.98 0.55 45.65 2.29
928 937 3.611766 AAGTAGGATTTCCCACACTCG 57.388 47.619 0.00 0.00 37.41 4.18
967 976 0.458370 CACGGTGCATCTCATGTCGA 60.458 55.000 0.00 0.00 0.00 4.20
1028 1037 2.203139 TGCGGTTGGGCCATATCG 60.203 61.111 7.26 11.99 36.97 2.92
1030 1039 1.108727 CATGTGCGGTTGGGCCATAT 61.109 55.000 7.26 0.00 36.97 1.78
1031 1040 1.752310 CATGTGCGGTTGGGCCATA 60.752 57.895 7.26 0.00 36.97 2.74
1160 1169 3.071206 GCTGAGCTCGAGTGGGGA 61.071 66.667 15.13 0.00 0.00 4.81
1201 1210 1.136884 CGTCGTCTTCTTGTTGCTTCG 60.137 52.381 0.00 0.00 0.00 3.79
1203 1212 2.218953 TCGTCGTCTTCTTGTTGCTT 57.781 45.000 0.00 0.00 0.00 3.91
1204 1213 2.128035 CTTCGTCGTCTTCTTGTTGCT 58.872 47.619 0.00 0.00 0.00 3.91
1205 1214 2.124903 TCTTCGTCGTCTTCTTGTTGC 58.875 47.619 0.00 0.00 0.00 4.17
1206 1215 4.042398 TCTTCTTCGTCGTCTTCTTGTTG 58.958 43.478 0.00 0.00 0.00 3.33
1207 1216 4.303086 TCTTCTTCGTCGTCTTCTTGTT 57.697 40.909 0.00 0.00 0.00 2.83
1208 1217 3.984508 TCTTCTTCGTCGTCTTCTTGT 57.015 42.857 0.00 0.00 0.00 3.16
1209 1218 3.120451 GCTTCTTCTTCGTCGTCTTCTTG 59.880 47.826 0.00 0.00 0.00 3.02
1214 1223 1.667467 GCTGCTTCTTCTTCGTCGTCT 60.667 52.381 0.00 0.00 0.00 4.18
1217 1226 0.712775 CTGCTGCTTCTTCTTCGTCG 59.287 55.000 0.00 0.00 0.00 5.12
1221 1230 1.068679 GTTGGCTGCTGCTTCTTCTTC 60.069 52.381 15.64 0.00 39.59 2.87
1238 1247 6.573664 TGGTGAAGTATCTTGATTTGGTTG 57.426 37.500 0.00 0.00 0.00 3.77
1518 1543 1.016627 GCGCATCAAATCAGTGGCTA 58.983 50.000 0.30 0.00 0.00 3.93
1529 2703 4.695993 TGTCAGCCCGCGCATCAA 62.696 61.111 8.75 0.00 37.52 2.57
1563 5046 0.165944 GCCGCGTGTATATCAATGGC 59.834 55.000 4.92 0.00 34.44 4.40
1600 5083 4.485163 CAAGTCAGATCACACACGACATA 58.515 43.478 0.00 0.00 0.00 2.29
1602 5085 2.742774 CAAGTCAGATCACACACGACA 58.257 47.619 0.00 0.00 0.00 4.35
1618 5101 0.038599 TGGATGCATGACTGGCAAGT 59.961 50.000 2.46 0.00 45.60 3.16
1818 5305 0.909623 ATTGAGGGGGTTAGGACACG 59.090 55.000 0.00 0.00 0.00 4.49
1891 5386 3.243771 CCTCCGACCGTAGATGCTTTTAT 60.244 47.826 0.00 0.00 0.00 1.40
1895 5392 2.017559 GCCTCCGACCGTAGATGCTT 62.018 60.000 0.00 0.00 0.00 3.91
1905 5402 2.593956 GGATATGGGGCCTCCGACC 61.594 68.421 0.00 0.00 38.76 4.79
1906 5408 3.069778 GGATATGGGGCCTCCGAC 58.930 66.667 0.00 0.00 38.76 4.79
1946 5448 1.697432 TCTATCTGGGCAATAACCGGG 59.303 52.381 6.32 0.00 35.03 5.73
1948 5450 4.260620 CGTTTTCTATCTGGGCAATAACCG 60.261 45.833 0.00 0.00 0.00 4.44
1952 5454 4.873827 GTGTCGTTTTCTATCTGGGCAATA 59.126 41.667 0.00 0.00 0.00 1.90
1954 5456 3.071479 GTGTCGTTTTCTATCTGGGCAA 58.929 45.455 0.00 0.00 0.00 4.52
1959 5461 3.435671 GGTTGGGTGTCGTTTTCTATCTG 59.564 47.826 0.00 0.00 0.00 2.90
1960 5462 3.671716 GGTTGGGTGTCGTTTTCTATCT 58.328 45.455 0.00 0.00 0.00 1.98
1965 5467 0.814812 TCCGGTTGGGTGTCGTTTTC 60.815 55.000 0.00 0.00 37.00 2.29
1994 5496 3.202829 AGGCTAAACGTTTGGACTGAA 57.797 42.857 29.47 4.62 35.50 3.02
2020 5523 1.078426 GGGCTGCGTATGAGGTTGT 60.078 57.895 0.00 0.00 0.00 3.32
2032 5535 1.074405 TCCATTCCAGATATGGGCTGC 59.926 52.381 6.52 0.00 42.32 5.25
2065 5568 3.053291 GGCGATTGGGTGCGTCAA 61.053 61.111 0.00 0.00 31.48 3.18
2090 5593 3.885814 GGATGGGCCTATCCGACA 58.114 61.111 30.20 5.12 37.48 4.35
2134 5637 0.106769 TGCCGTACGGGTGGAGTATA 60.107 55.000 33.98 0.00 38.44 1.47
2176 5679 2.688958 GAGAAGATGGGTAGTACAGCGT 59.311 50.000 2.06 0.00 0.00 5.07
2182 5685 3.136809 AGAGAGCGAGAAGATGGGTAGTA 59.863 47.826 0.00 0.00 0.00 1.82
2229 5732 0.931005 GACTCGTTGCCGAATCCATC 59.069 55.000 0.00 0.00 43.69 3.51
2231 5734 4.590487 GACTCGTTGCCGAATCCA 57.410 55.556 0.00 0.00 43.69 3.41
2238 5741 2.814183 ATCACGTCGGACTCGTTGCC 62.814 60.000 6.57 0.00 39.55 4.52
2239 5742 1.403972 GATCACGTCGGACTCGTTGC 61.404 60.000 6.57 0.00 39.55 4.17
2240 5743 1.126421 CGATCACGTCGGACTCGTTG 61.126 60.000 6.57 0.00 46.47 4.10
2241 5744 1.134075 CGATCACGTCGGACTCGTT 59.866 57.895 6.57 0.00 46.47 3.85
2242 5745 2.783275 CGATCACGTCGGACTCGT 59.217 61.111 6.57 0.00 46.47 4.18
2254 5757 2.434185 GCGTTGCCCAGTCGATCA 60.434 61.111 0.00 0.00 0.00 2.92
2288 5791 3.660501 TCGTACAACACAGATGAGCTT 57.339 42.857 0.00 0.00 0.00 3.74
2297 5800 1.893137 AGCTCCTCATCGTACAACACA 59.107 47.619 0.00 0.00 0.00 3.72
2344 5847 2.343758 CGCCCCTATCCATCCACG 59.656 66.667 0.00 0.00 0.00 4.94
2382 5888 3.005539 GCCTCTCTGGGCCACTGA 61.006 66.667 0.00 2.44 45.92 3.41
2436 5942 0.459585 GTCTAATCAAGCGCGGACCA 60.460 55.000 8.83 0.00 0.00 4.02
2446 5952 1.066430 GTCACCCTGCCGTCTAATCAA 60.066 52.381 0.00 0.00 0.00 2.57
2447 5953 0.535335 GTCACCCTGCCGTCTAATCA 59.465 55.000 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.