Multiple sequence alignment - TraesCS7D01G225600

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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 TraesCS7D01G225600 chr7D 100.000 3664 0 0 1 3664 185223497 185219834 0.000000e+00 6767.0
1 TraesCS7D01G225600 chr7D 95.455 770 28 3 1 763 337037812 337037043 0.000000e+00 1221.0
2 TraesCS7D01G225600 chr7D 90.000 830 63 10 2692 3517 185675374 185674561 0.000000e+00 1055.0
3 TraesCS7D01G225600 chr7D 90.884 713 54 4 880 1592 185368702 185368001 0.000000e+00 946.0
4 TraesCS7D01G225600 chr7D 100.000 427 0 0 4026 4452 185219472 185219046 0.000000e+00 789.0
5 TraesCS7D01G225600 chr7D 83.775 641 90 13 959 1592 185766134 185765501 2.960000e-166 595.0
6 TraesCS7D01G225600 chr7D 83.482 448 61 11 3105 3549 185374425 185373988 5.360000e-109 405.0
7 TraesCS7D01G225600 chr7D 83.255 424 65 4 3126 3548 185366228 185365810 6.990000e-103 385.0
8 TraesCS7D01G225600 chr7D 82.979 423 66 4 3126 3547 185763807 185763390 1.170000e-100 377.0
9 TraesCS7D01G225600 chr7D 89.931 288 25 4 2271 2558 185686298 185686015 7.040000e-98 368.0
10 TraesCS7D01G225600 chr7D 93.431 137 8 1 2554 2689 185675550 185675414 7.550000e-48 202.0
11 TraesCS7D01G225600 chr7B 94.395 2819 98 22 869 3664 327674418 327671637 0.000000e+00 4276.0
12 TraesCS7D01G225600 chr7B 96.253 427 11 4 4026 4451 327671389 327670967 0.000000e+00 695.0
13 TraesCS7D01G225600 chr7B 83.411 645 92 14 955 1592 328493957 328493321 6.420000e-163 584.0
14 TraesCS7D01G225600 chr7B 87.117 489 63 0 1104 1592 328166166 328165678 5.030000e-154 555.0
15 TraesCS7D01G225600 chr7A 93.913 2842 92 30 846 3664 192987687 192984904 0.000000e+00 4215.0
16 TraesCS7D01G225600 chr7A 90.584 754 51 10 844 1592 193504935 193504197 0.000000e+00 981.0
17 TraesCS7D01G225600 chr7A 90.135 740 62 4 853 1592 193380542 193379814 0.000000e+00 952.0
18 TraesCS7D01G225600 chr7A 84.135 624 85 12 976 1592 193591216 193590600 3.830000e-165 592.0
19 TraesCS7D01G225600 chr7A 90.909 352 11 2 4101 4452 192974080 192973750 1.890000e-123 453.0
20 TraesCS7D01G225600 chr7A 82.366 448 70 8 3105 3549 193588805 193588364 9.040000e-102 381.0
21 TraesCS7D01G225600 chr7A 83.290 383 61 3 3168 3549 193377973 193377593 2.550000e-92 350.0
22 TraesCS7D01G225600 chr7A 97.531 81 2 0 4026 4106 192984481 192984401 6.000000e-29 139.0
23 TraesCS7D01G225600 chr3D 95.866 774 21 5 1 763 338577399 338578172 0.000000e+00 1242.0
24 TraesCS7D01G225600 chr3D 91.253 766 57 9 1 763 237180668 237179910 0.000000e+00 1035.0
25 TraesCS7D01G225600 chr5D 92.338 770 42 14 1 763 183357256 183356497 0.000000e+00 1079.0
26 TraesCS7D01G225600 chr5D 91.580 772 53 11 1 767 185734216 185733452 0.000000e+00 1055.0
27 TraesCS7D01G225600 chr5D 91.134 767 59 8 1 764 195566003 195565243 0.000000e+00 1031.0
28 TraesCS7D01G225600 chr2D 91.906 766 53 8 1 763 270314912 270314153 0.000000e+00 1062.0
29 TraesCS7D01G225600 chr2D 91.384 766 58 7 1 763 269812730 269813490 0.000000e+00 1042.0
30 TraesCS7D01G225600 chr1D 91.775 766 52 8 1 763 124915245 124914488 0.000000e+00 1055.0
31 TraesCS7D01G225600 chr5A 92.453 53 4 0 4340 4392 514437146 514437094 4.780000e-10 76.8
32 TraesCS7D01G225600 chr3B 92.453 53 4 0 4340 4392 487603905 487603853 4.780000e-10 76.8


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 TraesCS7D01G225600 chr7D 185219046 185223497 4451 True 3778.0 6767 100.0000 1 4452 2 chr7D.!!$R4 4451
1 TraesCS7D01G225600 chr7D 337037043 337037812 769 True 1221.0 1221 95.4550 1 763 1 chr7D.!!$R3 762
2 TraesCS7D01G225600 chr7D 185365810 185368702 2892 True 665.5 946 87.0695 880 3548 2 chr7D.!!$R5 2668
3 TraesCS7D01G225600 chr7D 185674561 185675550 989 True 628.5 1055 91.7155 2554 3517 2 chr7D.!!$R6 963
4 TraesCS7D01G225600 chr7D 185763390 185766134 2744 True 486.0 595 83.3770 959 3547 2 chr7D.!!$R7 2588
5 TraesCS7D01G225600 chr7B 327670967 327674418 3451 True 2485.5 4276 95.3240 869 4451 2 chr7B.!!$R3 3582
6 TraesCS7D01G225600 chr7B 328493321 328493957 636 True 584.0 584 83.4110 955 1592 1 chr7B.!!$R2 637
7 TraesCS7D01G225600 chr7A 192984401 192987687 3286 True 2177.0 4215 95.7220 846 4106 2 chr7A.!!$R3 3260
8 TraesCS7D01G225600 chr7A 193504197 193504935 738 True 981.0 981 90.5840 844 1592 1 chr7A.!!$R2 748
9 TraesCS7D01G225600 chr7A 193377593 193380542 2949 True 651.0 952 86.7125 853 3549 2 chr7A.!!$R4 2696
10 TraesCS7D01G225600 chr7A 193588364 193591216 2852 True 486.5 592 83.2505 976 3549 2 chr7A.!!$R5 2573
11 TraesCS7D01G225600 chr3D 338577399 338578172 773 False 1242.0 1242 95.8660 1 763 1 chr3D.!!$F1 762
12 TraesCS7D01G225600 chr3D 237179910 237180668 758 True 1035.0 1035 91.2530 1 763 1 chr3D.!!$R1 762
13 TraesCS7D01G225600 chr5D 183356497 183357256 759 True 1079.0 1079 92.3380 1 763 1 chr5D.!!$R1 762
14 TraesCS7D01G225600 chr5D 185733452 185734216 764 True 1055.0 1055 91.5800 1 767 1 chr5D.!!$R2 766
15 TraesCS7D01G225600 chr5D 195565243 195566003 760 True 1031.0 1031 91.1340 1 764 1 chr5D.!!$R3 763
16 TraesCS7D01G225600 chr2D 270314153 270314912 759 True 1062.0 1062 91.9060 1 763 1 chr2D.!!$R1 762
17 TraesCS7D01G225600 chr2D 269812730 269813490 760 False 1042.0 1042 91.3840 1 763 1 chr2D.!!$F1 762
18 TraesCS7D01G225600 chr1D 124914488 124915245 757 True 1055.0 1055 91.7750 1 763 1 chr1D.!!$R1 762

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
835 851 0.108186 CTGCGTGTGCCCTCATCTAA 60.108 55.0 0.00 0.0 41.78 2.10 F
940 963 0.250424 TGGACACATGGTGCAGTCAG 60.250 55.0 0.00 0.0 43.49 3.51 F
2828 3682 0.775542 AAAACCGGGTAAAGCCTCCT 59.224 50.0 6.32 0.0 37.43 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2812 3666 0.546988 AGAAGGAGGCTTTACCCGGT 60.547 55.000 0.00 0.00 40.58 5.28 R
3072 3993 4.000331 AGTGAACTTCTGTCTGACATGG 58.000 45.455 11.45 7.04 0.00 3.66 R
4411 5407 3.078836 ATGCCAGCCCATGCCAAC 61.079 61.111 0.00 0.00 38.69 3.77 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
434 450 1.269413 GCTGCTGCTGTTGTTGACATT 60.269 47.619 8.53 0.00 37.69 2.71
515 531 3.477530 CCTTCTTCCGTTGGTTCTCTTT 58.522 45.455 0.00 0.00 0.00 2.52
560 576 2.592194 GTCTTCACGTGCATCTTCGTA 58.408 47.619 11.67 0.00 38.52 3.43
635 651 3.650070 TGTCTCGAGTGGATCATATGC 57.350 47.619 13.13 0.00 0.00 3.14
696 712 3.075998 GCTCGTGCTCGTGTCATG 58.924 61.111 8.17 0.00 38.33 3.07
703 719 1.296715 GCTCGTGTCATGGGTCCTT 59.703 57.895 0.00 0.00 0.00 3.36
728 744 3.181475 GGCTCTTGATGAGACGATGGTAA 60.181 47.826 0.00 0.00 45.39 2.85
769 785 3.215642 TGCTCCGCATCAATATCGG 57.784 52.632 0.00 0.00 44.16 4.18
770 786 0.392706 TGCTCCGCATCAATATCGGT 59.607 50.000 0.00 0.00 43.35 4.69
771 787 1.071605 GCTCCGCATCAATATCGGTC 58.928 55.000 0.00 0.00 43.35 4.79
772 788 1.340658 CTCCGCATCAATATCGGTCG 58.659 55.000 0.00 0.00 43.35 4.79
773 789 0.666274 TCCGCATCAATATCGGTCGC 60.666 55.000 0.00 0.00 43.35 5.19
774 790 1.412226 CGCATCAATATCGGTCGCG 59.588 57.895 0.00 0.00 34.89 5.87
775 791 1.781555 GCATCAATATCGGTCGCGG 59.218 57.895 6.13 0.00 0.00 6.46
776 792 0.944311 GCATCAATATCGGTCGCGGT 60.944 55.000 6.13 0.00 0.00 5.68
777 793 1.497991 CATCAATATCGGTCGCGGTT 58.502 50.000 6.13 0.00 0.00 4.44
778 794 1.864711 CATCAATATCGGTCGCGGTTT 59.135 47.619 6.13 0.00 0.00 3.27
779 795 2.867287 TCAATATCGGTCGCGGTTTA 57.133 45.000 6.13 0.00 0.00 2.01
780 796 3.374220 TCAATATCGGTCGCGGTTTAT 57.626 42.857 6.13 0.00 0.00 1.40
781 797 3.719924 TCAATATCGGTCGCGGTTTATT 58.280 40.909 6.13 0.78 0.00 1.40
782 798 3.737266 TCAATATCGGTCGCGGTTTATTC 59.263 43.478 6.13 0.00 0.00 1.75
783 799 2.138596 TATCGGTCGCGGTTTATTCC 57.861 50.000 6.13 0.00 0.00 3.01
784 800 0.462789 ATCGGTCGCGGTTTATTCCT 59.537 50.000 6.13 0.00 0.00 3.36
785 801 1.102154 TCGGTCGCGGTTTATTCCTA 58.898 50.000 6.13 0.00 0.00 2.94
786 802 1.476085 TCGGTCGCGGTTTATTCCTAA 59.524 47.619 6.13 0.00 0.00 2.69
787 803 1.589779 CGGTCGCGGTTTATTCCTAAC 59.410 52.381 6.13 0.00 0.00 2.34
788 804 2.620242 GGTCGCGGTTTATTCCTAACA 58.380 47.619 6.13 0.00 0.00 2.41
789 805 3.002102 GGTCGCGGTTTATTCCTAACAA 58.998 45.455 6.13 0.00 0.00 2.83
790 806 3.436359 GGTCGCGGTTTATTCCTAACAAA 59.564 43.478 6.13 0.00 0.00 2.83
791 807 4.083377 GGTCGCGGTTTATTCCTAACAAAA 60.083 41.667 6.13 0.00 0.00 2.44
792 808 5.451039 GTCGCGGTTTATTCCTAACAAAAA 58.549 37.500 6.13 0.00 0.00 1.94
793 809 5.340403 GTCGCGGTTTATTCCTAACAAAAAC 59.660 40.000 6.13 0.00 0.00 2.43
794 810 5.239087 TCGCGGTTTATTCCTAACAAAAACT 59.761 36.000 6.13 0.00 32.11 2.66
795 811 5.341196 CGCGGTTTATTCCTAACAAAAACTG 59.659 40.000 0.00 0.00 38.73 3.16
796 812 6.440436 GCGGTTTATTCCTAACAAAAACTGA 58.560 36.000 8.77 0.00 38.23 3.41
797 813 6.361481 GCGGTTTATTCCTAACAAAAACTGAC 59.639 38.462 8.77 0.00 38.23 3.51
798 814 6.575942 CGGTTTATTCCTAACAAAAACTGACG 59.424 38.462 0.00 0.00 38.23 4.35
799 815 6.859508 GGTTTATTCCTAACAAAAACTGACGG 59.140 38.462 0.00 0.00 32.11 4.79
800 816 6.563222 TTATTCCTAACAAAAACTGACGGG 57.437 37.500 0.00 0.00 0.00 5.28
801 817 2.223745 TCCTAACAAAAACTGACGGGC 58.776 47.619 0.00 0.00 0.00 6.13
802 818 2.158726 TCCTAACAAAAACTGACGGGCT 60.159 45.455 0.00 0.00 0.00 5.19
803 819 2.621526 CCTAACAAAAACTGACGGGCTT 59.378 45.455 0.00 0.00 0.00 4.35
804 820 3.067601 CCTAACAAAAACTGACGGGCTTT 59.932 43.478 0.00 0.00 0.00 3.51
805 821 2.863401 ACAAAAACTGACGGGCTTTC 57.137 45.000 0.00 0.00 0.00 2.62
806 822 2.096248 ACAAAAACTGACGGGCTTTCA 58.904 42.857 0.00 0.00 0.00 2.69
807 823 2.693074 ACAAAAACTGACGGGCTTTCAT 59.307 40.909 0.00 0.00 0.00 2.57
808 824 3.052036 CAAAAACTGACGGGCTTTCATG 58.948 45.455 0.00 0.00 0.00 3.07
809 825 1.247567 AAACTGACGGGCTTTCATGG 58.752 50.000 0.00 0.00 0.00 3.66
810 826 0.400213 AACTGACGGGCTTTCATGGA 59.600 50.000 0.00 0.00 0.00 3.41
811 827 0.321653 ACTGACGGGCTTTCATGGAC 60.322 55.000 0.00 0.00 0.00 4.02
812 828 1.002624 TGACGGGCTTTCATGGACC 60.003 57.895 0.00 0.00 0.00 4.46
813 829 1.002624 GACGGGCTTTCATGGACCA 60.003 57.895 0.00 0.00 0.00 4.02
814 830 1.303317 ACGGGCTTTCATGGACCAC 60.303 57.895 0.00 0.00 0.00 4.16
815 831 2.398554 CGGGCTTTCATGGACCACG 61.399 63.158 0.00 0.00 0.00 4.94
816 832 2.700773 GGGCTTTCATGGACCACGC 61.701 63.158 0.00 0.00 0.00 5.34
817 833 1.675641 GGCTTTCATGGACCACGCT 60.676 57.895 0.00 0.00 0.00 5.07
818 834 1.503542 GCTTTCATGGACCACGCTG 59.496 57.895 0.00 0.00 0.00 5.18
819 835 1.503542 CTTTCATGGACCACGCTGC 59.496 57.895 0.00 0.00 0.00 5.25
820 836 2.244436 CTTTCATGGACCACGCTGCG 62.244 60.000 21.91 21.91 0.00 5.18
821 837 3.529341 TTCATGGACCACGCTGCGT 62.529 57.895 23.57 23.57 42.36 5.24
832 848 3.503363 GCTGCGTGTGCCCTCATC 61.503 66.667 0.00 0.00 41.78 2.92
833 849 2.267006 CTGCGTGTGCCCTCATCT 59.733 61.111 0.00 0.00 41.78 2.90
834 850 1.517361 CTGCGTGTGCCCTCATCTA 59.483 57.895 0.00 0.00 41.78 1.98
835 851 0.108186 CTGCGTGTGCCCTCATCTAA 60.108 55.000 0.00 0.00 41.78 2.10
836 852 0.541392 TGCGTGTGCCCTCATCTAAT 59.459 50.000 0.00 0.00 41.78 1.73
837 853 1.065491 TGCGTGTGCCCTCATCTAATT 60.065 47.619 0.00 0.00 41.78 1.40
838 854 1.331756 GCGTGTGCCCTCATCTAATTG 59.668 52.381 0.00 0.00 33.98 2.32
839 855 1.331756 CGTGTGCCCTCATCTAATTGC 59.668 52.381 0.00 0.00 0.00 3.56
840 856 2.368439 GTGTGCCCTCATCTAATTGCA 58.632 47.619 0.00 0.00 0.00 4.08
841 857 2.098117 GTGTGCCCTCATCTAATTGCAC 59.902 50.000 5.54 5.54 46.85 4.57
842 858 1.678101 GTGCCCTCATCTAATTGCACC 59.322 52.381 0.00 0.00 42.33 5.01
843 859 1.322442 GCCCTCATCTAATTGCACCC 58.678 55.000 0.00 0.00 0.00 4.61
844 860 1.410083 GCCCTCATCTAATTGCACCCA 60.410 52.381 0.00 0.00 0.00 4.51
940 963 0.250424 TGGACACATGGTGCAGTCAG 60.250 55.000 0.00 0.00 43.49 3.51
1032 1059 2.384309 CGGCGTTCGCATGGTTACA 61.384 57.895 18.46 0.00 0.00 2.41
1088 1115 3.118775 AGGCTCCAGGTTTGTTTGTTTTC 60.119 43.478 0.00 0.00 0.00 2.29
1089 1116 3.118775 GGCTCCAGGTTTGTTTGTTTTCT 60.119 43.478 0.00 0.00 0.00 2.52
1090 1117 4.098807 GGCTCCAGGTTTGTTTGTTTTCTA 59.901 41.667 0.00 0.00 0.00 2.10
1091 1118 5.041287 GCTCCAGGTTTGTTTGTTTTCTAC 58.959 41.667 0.00 0.00 0.00 2.59
1135 1166 1.211969 CCTGCACTGTGCTGCAATC 59.788 57.895 30.43 3.50 46.46 2.67
1329 1396 4.138290 CTCTAAGCTTCATCTCCGAGGTA 58.862 47.826 0.00 0.00 0.00 3.08
1379 1446 4.736896 GGAAGAGGAACGGCGCGT 62.737 66.667 6.90 0.00 43.97 6.01
1487 1554 1.153229 GGAAAGATACGCCGCCCTT 60.153 57.895 0.00 0.00 0.00 3.95
1652 1823 9.444668 TTTAGATACTACCTACTACTCTCTCCA 57.555 37.037 0.00 0.00 0.00 3.86
1729 1901 5.535783 TGTTGATATTATGGGCATGTTCTGG 59.464 40.000 0.00 0.00 0.00 3.86
1760 1932 2.887152 ACTTCTTGCTCCACAACATTCC 59.113 45.455 0.00 0.00 33.68 3.01
2116 2399 9.700831 ATTTCCTATATTATGCCCAAGATTACC 57.299 33.333 0.00 0.00 0.00 2.85
2117 2400 6.884832 TCCTATATTATGCCCAAGATTACCG 58.115 40.000 0.00 0.00 0.00 4.02
2118 2401 6.442564 TCCTATATTATGCCCAAGATTACCGT 59.557 38.462 0.00 0.00 0.00 4.83
2119 2402 7.037873 TCCTATATTATGCCCAAGATTACCGTT 60.038 37.037 0.00 0.00 0.00 4.44
2120 2403 7.610305 CCTATATTATGCCCAAGATTACCGTTT 59.390 37.037 0.00 0.00 0.00 3.60
2121 2404 5.767816 ATTATGCCCAAGATTACCGTTTC 57.232 39.130 0.00 0.00 0.00 2.78
2122 2405 2.570415 TGCCCAAGATTACCGTTTCA 57.430 45.000 0.00 0.00 0.00 2.69
2123 2406 2.432444 TGCCCAAGATTACCGTTTCAG 58.568 47.619 0.00 0.00 0.00 3.02
2266 3029 7.084486 CGAAATATCTCAACGATATCCTGTCA 58.916 38.462 0.00 0.00 43.00 3.58
2284 3047 5.063438 CCTGTCACATTATAAGAACACACCG 59.937 44.000 0.00 0.00 0.00 4.94
2317 3084 2.034124 AGCTTCACCATGCAAAGTTGT 58.966 42.857 0.00 0.00 0.00 3.32
2465 3278 4.454678 TCTCAAGTTGCACTCACTTGAAT 58.545 39.130 25.05 0.00 45.94 2.57
2812 3666 2.294512 TGTGCCACGTATGATGCAAAAA 59.705 40.909 0.00 0.00 35.16 1.94
2827 3681 1.271379 CAAAAACCGGGTAAAGCCTCC 59.729 52.381 6.32 0.00 37.43 4.30
2828 3682 0.775542 AAAACCGGGTAAAGCCTCCT 59.224 50.000 6.32 0.00 37.43 3.69
2829 3683 0.775542 AAACCGGGTAAAGCCTCCTT 59.224 50.000 6.32 0.00 37.43 3.36
3089 4010 2.705658 TCCACCATGTCAGACAGAAGTT 59.294 45.455 9.64 0.00 0.00 2.66
3117 4041 9.575783 ACTTTTGAACGCTAAAATAAGAACAAA 57.424 25.926 0.00 0.00 0.00 2.83
3259 4183 0.530744 CATCCGTGAAAGAGGTCCGA 59.469 55.000 0.00 0.00 0.00 4.55
3353 4277 1.044611 TGACTTGGACGGTGATGTGA 58.955 50.000 0.00 0.00 0.00 3.58
3354 4278 1.623311 TGACTTGGACGGTGATGTGAT 59.377 47.619 0.00 0.00 0.00 3.06
3473 4397 1.917303 GACTTGTTTGTGGTGTTTGCG 59.083 47.619 0.00 0.00 0.00 4.85
4270 5265 9.754382 AATTTACAGGTGCATGAATTCATAATC 57.246 29.630 20.32 12.14 34.26 1.75
4332 5327 3.181501 ACAATTCCAAATATGCCACGACG 60.182 43.478 0.00 0.00 0.00 5.12
4333 5328 2.388310 TTCCAAATATGCCACGACGA 57.612 45.000 0.00 0.00 0.00 4.20
4334 5329 2.388310 TCCAAATATGCCACGACGAA 57.612 45.000 0.00 0.00 0.00 3.85
4389 5385 2.282745 ACTTGGAGCTGCCTTGCC 60.283 61.111 1.53 0.00 37.63 4.52
4397 5393 2.960170 CTGCCTTGCCACTTGAGC 59.040 61.111 0.00 0.00 0.00 4.26
4411 5407 4.142902 CCACTTGAGCGTATAGTTGTTTGG 60.143 45.833 0.00 0.00 0.00 3.28
4425 5421 2.215625 TTTGGTTGGCATGGGCTGG 61.216 57.895 0.00 0.00 40.87 4.85
4451 5447 1.832883 TCTTGTGTGCTTGTTGTGGT 58.167 45.000 0.00 0.00 0.00 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
380 396 1.762460 CTACAGGGCCCGGACATCT 60.762 63.158 30.18 8.18 0.00 2.90
434 450 2.674754 GACATCCGGCCCCTGAAA 59.325 61.111 0.00 0.00 0.00 2.69
515 531 1.595311 AGCCACCAAGTCCATGGATA 58.405 50.000 19.62 0.00 43.54 2.59
560 576 1.059913 CAGGTGTCAAGAGGACCCTT 58.940 55.000 0.00 0.00 46.38 3.95
635 651 6.210078 GTGACTTCCTTCCTTAGTGATATCG 58.790 44.000 0.00 0.00 0.00 2.92
696 712 1.821136 CATCAAGAGCCAAAAGGACCC 59.179 52.381 0.00 0.00 0.00 4.46
703 719 3.264947 CATCGTCTCATCAAGAGCCAAA 58.735 45.455 0.00 0.00 44.35 3.28
728 744 2.251818 CTACGATCATCCCCATGGACT 58.748 52.381 15.22 0.00 45.58 3.85
764 780 1.682854 AGGAATAAACCGCGACCGATA 59.317 47.619 8.23 0.00 36.29 2.92
767 783 1.589779 GTTAGGAATAAACCGCGACCG 59.410 52.381 8.23 0.00 34.73 4.79
768 784 2.620242 TGTTAGGAATAAACCGCGACC 58.380 47.619 8.23 0.00 34.73 4.79
769 785 4.666928 TTTGTTAGGAATAAACCGCGAC 57.333 40.909 8.23 0.00 34.73 5.19
770 786 5.239087 AGTTTTTGTTAGGAATAAACCGCGA 59.761 36.000 8.23 0.00 34.73 5.87
771 787 5.341196 CAGTTTTTGTTAGGAATAAACCGCG 59.659 40.000 0.00 0.00 34.73 6.46
772 788 6.361481 GTCAGTTTTTGTTAGGAATAAACCGC 59.639 38.462 0.00 0.00 34.73 5.68
773 789 6.575942 CGTCAGTTTTTGTTAGGAATAAACCG 59.424 38.462 0.00 0.00 34.73 4.44
774 790 6.859508 CCGTCAGTTTTTGTTAGGAATAAACC 59.140 38.462 0.00 0.00 30.93 3.27
775 791 6.859508 CCCGTCAGTTTTTGTTAGGAATAAAC 59.140 38.462 0.00 0.00 0.00 2.01
776 792 6.515365 GCCCGTCAGTTTTTGTTAGGAATAAA 60.515 38.462 0.00 0.00 0.00 1.40
777 793 5.048573 GCCCGTCAGTTTTTGTTAGGAATAA 60.049 40.000 0.00 0.00 0.00 1.40
778 794 4.456566 GCCCGTCAGTTTTTGTTAGGAATA 59.543 41.667 0.00 0.00 0.00 1.75
779 795 3.254903 GCCCGTCAGTTTTTGTTAGGAAT 59.745 43.478 0.00 0.00 0.00 3.01
780 796 2.619646 GCCCGTCAGTTTTTGTTAGGAA 59.380 45.455 0.00 0.00 0.00 3.36
781 797 2.158726 AGCCCGTCAGTTTTTGTTAGGA 60.159 45.455 0.00 0.00 0.00 2.94
782 798 2.227194 AGCCCGTCAGTTTTTGTTAGG 58.773 47.619 0.00 0.00 0.00 2.69
783 799 3.982576 AAGCCCGTCAGTTTTTGTTAG 57.017 42.857 0.00 0.00 0.00 2.34
784 800 3.695060 TGAAAGCCCGTCAGTTTTTGTTA 59.305 39.130 0.00 0.00 0.00 2.41
785 801 2.494073 TGAAAGCCCGTCAGTTTTTGTT 59.506 40.909 0.00 0.00 0.00 2.83
786 802 2.096248 TGAAAGCCCGTCAGTTTTTGT 58.904 42.857 0.00 0.00 0.00 2.83
787 803 2.861462 TGAAAGCCCGTCAGTTTTTG 57.139 45.000 0.00 0.00 0.00 2.44
788 804 2.035832 CCATGAAAGCCCGTCAGTTTTT 59.964 45.455 0.00 0.00 0.00 1.94
789 805 1.613437 CCATGAAAGCCCGTCAGTTTT 59.387 47.619 0.00 0.00 0.00 2.43
790 806 1.202879 TCCATGAAAGCCCGTCAGTTT 60.203 47.619 0.00 0.00 0.00 2.66
791 807 0.400213 TCCATGAAAGCCCGTCAGTT 59.600 50.000 0.00 0.00 0.00 3.16
792 808 0.321653 GTCCATGAAAGCCCGTCAGT 60.322 55.000 0.00 0.00 0.00 3.41
793 809 1.026718 GGTCCATGAAAGCCCGTCAG 61.027 60.000 0.00 0.00 0.00 3.51
794 810 1.002624 GGTCCATGAAAGCCCGTCA 60.003 57.895 0.00 0.00 0.00 4.35
795 811 1.002624 TGGTCCATGAAAGCCCGTC 60.003 57.895 0.00 0.00 0.00 4.79
796 812 1.303317 GTGGTCCATGAAAGCCCGT 60.303 57.895 0.00 0.00 0.00 5.28
797 813 2.398554 CGTGGTCCATGAAAGCCCG 61.399 63.158 4.96 0.00 0.00 6.13
798 814 2.700773 GCGTGGTCCATGAAAGCCC 61.701 63.158 15.72 0.00 0.00 5.19
799 815 1.675641 AGCGTGGTCCATGAAAGCC 60.676 57.895 15.72 0.00 0.00 4.35
800 816 1.503542 CAGCGTGGTCCATGAAAGC 59.496 57.895 15.72 6.69 0.00 3.51
801 817 1.503542 GCAGCGTGGTCCATGAAAG 59.496 57.895 15.72 4.56 0.00 2.62
802 818 2.324330 CGCAGCGTGGTCCATGAAA 61.324 57.895 15.72 0.00 0.00 2.69
803 819 2.741985 CGCAGCGTGGTCCATGAA 60.742 61.111 15.72 0.00 0.00 2.57
804 820 4.002506 ACGCAGCGTGGTCCATGA 62.003 61.111 22.28 0.00 39.18 3.07
815 831 2.578163 TAGATGAGGGCACACGCAGC 62.578 60.000 0.00 0.00 41.24 5.25
816 832 0.108186 TTAGATGAGGGCACACGCAG 60.108 55.000 0.00 0.00 41.24 5.18
817 833 0.541392 ATTAGATGAGGGCACACGCA 59.459 50.000 0.00 0.00 41.24 5.24
818 834 1.331756 CAATTAGATGAGGGCACACGC 59.668 52.381 0.00 0.00 37.44 5.34
819 835 1.331756 GCAATTAGATGAGGGCACACG 59.668 52.381 0.00 0.00 0.00 4.49
820 836 2.368439 TGCAATTAGATGAGGGCACAC 58.632 47.619 0.00 0.00 0.00 3.82
821 837 2.804986 TGCAATTAGATGAGGGCACA 57.195 45.000 0.00 0.00 0.00 4.57
823 839 1.410083 GGGTGCAATTAGATGAGGGCA 60.410 52.381 0.00 0.00 0.00 5.36
824 840 1.322442 GGGTGCAATTAGATGAGGGC 58.678 55.000 0.00 0.00 0.00 5.19
825 841 2.734755 TGGGTGCAATTAGATGAGGG 57.265 50.000 0.00 0.00 0.00 4.30
826 842 5.380043 AGTAATGGGTGCAATTAGATGAGG 58.620 41.667 0.00 0.00 0.00 3.86
827 843 5.178252 CGAGTAATGGGTGCAATTAGATGAG 59.822 44.000 0.00 0.00 0.00 2.90
828 844 5.056480 CGAGTAATGGGTGCAATTAGATGA 58.944 41.667 0.00 0.00 0.00 2.92
829 845 4.816385 ACGAGTAATGGGTGCAATTAGATG 59.184 41.667 0.00 0.00 0.00 2.90
830 846 4.816385 CACGAGTAATGGGTGCAATTAGAT 59.184 41.667 0.00 0.00 0.00 1.98
831 847 4.188462 CACGAGTAATGGGTGCAATTAGA 58.812 43.478 0.00 0.00 0.00 2.10
832 848 3.938963 ACACGAGTAATGGGTGCAATTAG 59.061 43.478 0.00 0.00 35.11 1.73
833 849 3.945346 ACACGAGTAATGGGTGCAATTA 58.055 40.909 0.00 0.00 35.11 1.40
834 850 2.790433 ACACGAGTAATGGGTGCAATT 58.210 42.857 0.00 0.00 35.11 2.32
835 851 2.489938 ACACGAGTAATGGGTGCAAT 57.510 45.000 0.00 0.00 35.11 3.56
836 852 2.264005 AACACGAGTAATGGGTGCAA 57.736 45.000 0.00 0.00 35.11 4.08
837 853 1.876799 CAAACACGAGTAATGGGTGCA 59.123 47.619 0.00 0.00 35.11 4.57
838 854 1.877443 ACAAACACGAGTAATGGGTGC 59.123 47.619 0.00 0.00 35.11 5.01
839 855 2.225491 CCACAAACACGAGTAATGGGTG 59.775 50.000 0.00 0.00 37.67 4.61
840 856 2.500229 CCACAAACACGAGTAATGGGT 58.500 47.619 0.00 0.00 0.00 4.51
841 857 1.810151 CCCACAAACACGAGTAATGGG 59.190 52.381 12.54 12.54 37.71 4.00
842 858 1.810151 CCCCACAAACACGAGTAATGG 59.190 52.381 0.00 0.00 0.00 3.16
843 859 1.810151 CCCCCACAAACACGAGTAATG 59.190 52.381 0.00 0.00 0.00 1.90
844 860 1.422402 ACCCCCACAAACACGAGTAAT 59.578 47.619 0.00 0.00 0.00 1.89
901 917 7.173562 GTGTCCAGTATAGAGTATAGACCACAG 59.826 44.444 0.00 0.00 0.00 3.66
940 963 1.657822 GGGCTACAAGCTTGCTAGAC 58.342 55.000 26.27 24.38 41.99 2.59
1032 1059 3.030652 CTGTTTTCGCCGTTGCCT 58.969 55.556 0.00 0.00 0.00 4.75
1088 1115 3.181434 ACCTGGAGCCTCTCATCTAGTAG 60.181 52.174 0.00 0.00 31.08 2.57
1089 1116 2.786445 ACCTGGAGCCTCTCATCTAGTA 59.214 50.000 0.00 0.00 31.08 1.82
1090 1117 1.573376 ACCTGGAGCCTCTCATCTAGT 59.427 52.381 0.00 0.00 31.08 2.57
1091 1118 2.380064 ACCTGGAGCCTCTCATCTAG 57.620 55.000 0.00 0.00 31.08 2.43
1135 1166 9.690428 AGCAAATTATTCATGCAACGAGAGTGG 62.690 40.741 4.70 0.00 42.45 4.00
1329 1396 1.194781 AGGAGTGGACTGCACCGATT 61.195 55.000 0.87 0.00 36.72 3.34
1379 1446 1.420138 GGAAGAACTGGACCTCCACAA 59.580 52.381 0.00 0.00 42.01 3.33
1500 1567 1.069258 GTAGTATGACCGGGGCAGC 59.931 63.158 9.30 3.67 0.00 5.25
1537 1604 0.832135 TGGAAGAAGTGGACGCTCCT 60.832 55.000 5.77 0.00 37.46 3.69
1631 1802 8.277720 TGAATGGAGAGAGTAGTAGGTAGTAT 57.722 38.462 0.00 0.00 0.00 2.12
1632 1803 7.687383 TGAATGGAGAGAGTAGTAGGTAGTA 57.313 40.000 0.00 0.00 0.00 1.82
1633 1804 6.578313 TGAATGGAGAGAGTAGTAGGTAGT 57.422 41.667 0.00 0.00 0.00 2.73
1634 1805 7.883391 TTTGAATGGAGAGAGTAGTAGGTAG 57.117 40.000 0.00 0.00 0.00 3.18
1635 1806 8.660295 TTTTTGAATGGAGAGAGTAGTAGGTA 57.340 34.615 0.00 0.00 0.00 3.08
1636 1807 7.554959 TTTTTGAATGGAGAGAGTAGTAGGT 57.445 36.000 0.00 0.00 0.00 3.08
1729 1901 2.614229 GGAGCAAGAAGTTGGAGAGGTC 60.614 54.545 0.00 0.00 33.87 3.85
1760 1932 1.585668 CGTGAATCTAGCTTCGCACTG 59.414 52.381 17.41 1.04 35.79 3.66
1870 2042 0.908198 CTCCTGTTCCAAGGCTAGCT 59.092 55.000 15.72 0.00 37.24 3.32
2007 2289 5.456548 TTTGTGTTATCGTACTCACTCCA 57.543 39.130 0.00 0.00 0.00 3.86
2113 2396 7.042797 ACTACAAGAAAGTACTGAAACGGTA 57.957 36.000 0.00 0.00 0.00 4.02
2114 2397 5.910614 ACTACAAGAAAGTACTGAAACGGT 58.089 37.500 0.00 0.00 0.00 4.83
2115 2398 6.700520 AGAACTACAAGAAAGTACTGAAACGG 59.299 38.462 0.00 0.00 0.00 4.44
2116 2399 7.648510 AGAGAACTACAAGAAAGTACTGAAACG 59.351 37.037 0.00 0.00 0.00 3.60
2117 2400 8.874744 AGAGAACTACAAGAAAGTACTGAAAC 57.125 34.615 0.00 0.00 0.00 2.78
2118 2401 8.142551 GGAGAGAACTACAAGAAAGTACTGAAA 58.857 37.037 0.00 0.00 0.00 2.69
2119 2402 7.521748 CGGAGAGAACTACAAGAAAGTACTGAA 60.522 40.741 0.00 0.00 0.00 3.02
2120 2403 6.072618 CGGAGAGAACTACAAGAAAGTACTGA 60.073 42.308 0.00 0.00 0.00 3.41
2121 2404 6.072618 TCGGAGAGAACTACAAGAAAGTACTG 60.073 42.308 0.00 0.00 0.00 2.74
2122 2405 6.002704 TCGGAGAGAACTACAAGAAAGTACT 58.997 40.000 0.00 0.00 0.00 2.73
2123 2406 6.251655 TCGGAGAGAACTACAAGAAAGTAC 57.748 41.667 0.00 0.00 0.00 2.73
2266 3029 5.588648 CCATTCCGGTGTGTTCTTATAATGT 59.411 40.000 0.00 0.00 0.00 2.71
2284 3047 2.489722 GGTGAAGCTTTCAGACCATTCC 59.510 50.000 0.00 0.00 41.01 3.01
2297 3064 2.034124 ACAACTTTGCATGGTGAAGCT 58.966 42.857 11.51 0.00 0.00 3.74
2317 3084 7.448420 TCCATGGAAGCAAATTGAATTGTTTA 58.552 30.769 13.46 0.00 34.45 2.01
2465 3278 4.299586 TCCAATGTAGATGTTGCCTTCA 57.700 40.909 0.00 0.00 0.00 3.02
2812 3666 0.546988 AGAAGGAGGCTTTACCCGGT 60.547 55.000 0.00 0.00 40.58 5.28
3072 3993 4.000331 AGTGAACTTCTGTCTGACATGG 58.000 45.455 11.45 7.04 0.00 3.66
3089 4010 8.399425 TGTTCTTATTTTAGCGTTCAAAAGTGA 58.601 29.630 0.00 0.00 0.00 3.41
3117 4041 5.710099 TGAGAAATCTTATTTTGCGGAACCT 59.290 36.000 0.00 0.00 0.00 3.50
3259 4183 4.530161 AGCCTACTCTTGTTGATCAACTCT 59.470 41.667 32.57 16.12 41.67 3.24
3353 4277 4.248859 CGCTGCCAGCATAATCTAGTAAT 58.751 43.478 18.21 0.00 42.58 1.89
3354 4278 3.554960 CCGCTGCCAGCATAATCTAGTAA 60.555 47.826 18.21 0.00 42.58 2.24
3473 4397 1.470098 AGATGCTTTGCAACGATGGAC 59.530 47.619 7.19 0.00 43.62 4.02
3579 4503 3.043418 GGCCTCCCACTTACAATACCTA 58.957 50.000 0.00 0.00 0.00 3.08
4267 5262 6.878317 TGACCGAATGATTTACTCTCTGATT 58.122 36.000 0.00 0.00 0.00 2.57
4270 5265 7.545362 AATTGACCGAATGATTTACTCTCTG 57.455 36.000 0.00 0.00 0.00 3.35
4317 5312 4.028383 GTGATTTCGTCGTGGCATATTTG 58.972 43.478 0.00 0.00 0.00 2.32
4332 5327 6.021468 CGACGGAAAAATATGCAAGTGATTTC 60.021 38.462 0.00 0.00 0.00 2.17
4333 5328 5.799936 CGACGGAAAAATATGCAAGTGATTT 59.200 36.000 0.00 0.00 0.00 2.17
4334 5329 5.106317 ACGACGGAAAAATATGCAAGTGATT 60.106 36.000 0.00 0.00 0.00 2.57
4389 5385 4.451096 ACCAAACAACTATACGCTCAAGTG 59.549 41.667 0.00 0.00 0.00 3.16
4397 5393 4.411327 CATGCCAACCAAACAACTATACG 58.589 43.478 0.00 0.00 0.00 3.06
4411 5407 3.078836 ATGCCAGCCCATGCCAAC 61.079 61.111 0.00 0.00 38.69 3.77
4425 5421 3.293311 ACAAGCACACAAGAATCATGC 57.707 42.857 0.00 0.00 36.52 4.06


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

AutoCloner maintained by Alex Coulton.