Multiple sequence alignment - TraesCS5D01G453100

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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 TraesCS5D01G453100 chr5D 100.000 3071 0 0 1 3071 500685659 500682589 0.000000e+00 5672.0
1 TraesCS5D01G453100 chr5D 87.102 597 65 9 46 631 482593694 482593099 0.000000e+00 665.0
2 TraesCS5D01G453100 chr5D 83.871 527 67 8 34 549 507619758 507620277 1.280000e-133 486.0
3 TraesCS5D01G453100 chr5D 84.401 359 53 2 2602 2957 500648514 500648156 1.750000e-92 350.0
4 TraesCS5D01G453100 chr5D 92.727 110 8 0 755 864 500684866 500684757 3.170000e-35 159.0
5 TraesCS5D01G453100 chr5D 92.727 110 8 0 794 903 500684905 500684796 3.170000e-35 159.0
6 TraesCS5D01G453100 chr5B 90.734 1403 80 23 793 2161 622325368 622323982 0.000000e+00 1825.0
7 TraesCS5D01G453100 chr5B 93.060 634 37 4 2443 3071 622075631 622075000 0.000000e+00 920.0
8 TraesCS5D01G453100 chr5B 86.059 538 66 6 122 659 534913295 534913823 1.240000e-158 569.0
9 TraesCS5D01G453100 chr5B 85.932 526 65 8 146 671 490547385 490547901 1.240000e-153 553.0
10 TraesCS5D01G453100 chr5B 84.807 362 47 7 2602 2957 622064194 622063835 1.050000e-94 357.0
11 TraesCS5D01G453100 chr5B 90.000 180 16 2 685 862 622325438 622325259 6.620000e-57 231.0
12 TraesCS5D01G453100 chr5B 90.541 74 6 1 2137 2210 622075942 622075870 2.520000e-16 97.1
13 TraesCS5D01G453100 chr5A 93.967 1094 49 8 1134 2220 624963727 624964810 0.000000e+00 1639.0
14 TraesCS5D01G453100 chr5A 93.352 1068 48 16 1134 2187 627026651 627025593 0.000000e+00 1557.0
15 TraesCS5D01G453100 chr5A 91.617 668 29 12 2414 3071 624964941 624965591 0.000000e+00 898.0
16 TraesCS5D01G453100 chr5A 82.067 329 39 8 825 1142 627027532 627027213 2.350000e-66 263.0
17 TraesCS5D01G453100 chr5A 90.173 173 17 0 970 1142 624962966 624963138 3.080000e-55 226.0
18 TraesCS5D01G453100 chr5A 82.960 223 38 0 2607 2829 627024877 627024655 5.190000e-48 202.0
19 TraesCS5D01G453100 chr5A 81.405 242 24 10 2848 3071 627016637 627016399 8.750000e-41 178.0
20 TraesCS5D01G453100 chr2D 89.366 536 57 0 142 677 247848128 247847593 0.000000e+00 675.0
21 TraesCS5D01G453100 chr7D 87.638 542 63 4 132 671 558166368 558165829 7.230000e-176 627.0
22 TraesCS5D01G453100 chrUn 86.617 538 63 6 122 659 363763492 363762964 1.230000e-163 586.0
23 TraesCS5D01G453100 chrUn 86.431 538 64 6 122 659 80092593 80092065 5.710000e-162 580.0
24 TraesCS5D01G453100 chr3B 85.156 512 67 7 147 654 758722111 758721605 1.630000e-142 516.0
25 TraesCS5D01G453100 chr3B 85.156 512 67 7 147 654 759063710 759063204 1.630000e-142 516.0
26 TraesCS5D01G453100 chr2B 77.286 339 50 15 15 329 756154435 756154100 1.130000e-39 174.0
27 TraesCS5D01G453100 chr4B 74.678 466 79 22 2619 3071 642960344 642959905 1.460000e-38 171.0
28 TraesCS5D01G453100 chr4D 84.524 84 13 0 2988 3071 499510181 499510264 1.960000e-12 84.2


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 TraesCS5D01G453100 chr5D 500682589 500685659 3070 True 1996.666667 5672 95.151333 1 3071 3 chr5D.!!$R3 3070
1 TraesCS5D01G453100 chr5D 482593099 482593694 595 True 665.000000 665 87.102000 46 631 1 chr5D.!!$R1 585
2 TraesCS5D01G453100 chr5D 507619758 507620277 519 False 486.000000 486 83.871000 34 549 1 chr5D.!!$F1 515
3 TraesCS5D01G453100 chr5B 622323982 622325438 1456 True 1028.000000 1825 90.367000 685 2161 2 chr5B.!!$R3 1476
4 TraesCS5D01G453100 chr5B 534913295 534913823 528 False 569.000000 569 86.059000 122 659 1 chr5B.!!$F2 537
5 TraesCS5D01G453100 chr5B 490547385 490547901 516 False 553.000000 553 85.932000 146 671 1 chr5B.!!$F1 525
6 TraesCS5D01G453100 chr5B 622075000 622075942 942 True 508.550000 920 91.800500 2137 3071 2 chr5B.!!$R2 934
7 TraesCS5D01G453100 chr5A 624962966 624965591 2625 False 921.000000 1639 91.919000 970 3071 3 chr5A.!!$F1 2101
8 TraesCS5D01G453100 chr5A 627024655 627027532 2877 True 674.000000 1557 86.126333 825 2829 3 chr5A.!!$R2 2004
9 TraesCS5D01G453100 chr2D 247847593 247848128 535 True 675.000000 675 89.366000 142 677 1 chr2D.!!$R1 535
10 TraesCS5D01G453100 chr7D 558165829 558166368 539 True 627.000000 627 87.638000 132 671 1 chr7D.!!$R1 539
11 TraesCS5D01G453100 chrUn 363762964 363763492 528 True 586.000000 586 86.617000 122 659 1 chrUn.!!$R2 537
12 TraesCS5D01G453100 chrUn 80092065 80092593 528 True 580.000000 580 86.431000 122 659 1 chrUn.!!$R1 537
13 TraesCS5D01G453100 chr3B 758721605 758722111 506 True 516.000000 516 85.156000 147 654 1 chr3B.!!$R1 507
14 TraesCS5D01G453100 chr3B 759063204 759063710 506 True 516.000000 516 85.156000 147 654 1 chr3B.!!$R2 507

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
778 810 0.033405 TCCTACTCGGAGTTGGAGGG 60.033 60.0 29.39 17.51 43.43 4.30 F
786 818 0.034089 GGAGTTGGAGGGATTGGGTG 60.034 60.0 0.00 0.00 0.00 4.61 F
789 821 0.676782 GTTGGAGGGATTGGGTGACG 60.677 60.0 0.00 0.00 0.00 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2012 2693 0.025001 CGTTTCACGATCGACCATGC 59.975 55.0 24.34 6.22 46.05 4.06 R
2037 2718 0.109342 AGCCCACAAGACTGTTGAGG 59.891 55.0 0.00 0.00 31.64 3.86 R
2460 3453 0.512952 CTTGAACTTTCGTGGAGGCG 59.487 55.0 0.00 0.00 0.00 5.52 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
22 23 5.968387 CTTAACCACATGACTCGTTATCC 57.032 43.478 0.00 0.00 0.00 2.59
23 24 3.973206 AACCACATGACTCGTTATCCA 57.027 42.857 0.00 0.00 0.00 3.41
24 25 3.526931 ACCACATGACTCGTTATCCAG 57.473 47.619 0.00 0.00 0.00 3.86
25 26 2.168521 ACCACATGACTCGTTATCCAGG 59.831 50.000 0.00 0.00 0.00 4.45
26 27 2.430694 CCACATGACTCGTTATCCAGGA 59.569 50.000 0.00 0.00 0.00 3.86
27 28 3.118775 CCACATGACTCGTTATCCAGGAA 60.119 47.826 0.00 0.00 0.00 3.36
28 29 4.503910 CACATGACTCGTTATCCAGGAAA 58.496 43.478 0.00 0.00 0.00 3.13
29 30 4.330074 CACATGACTCGTTATCCAGGAAAC 59.670 45.833 0.00 0.00 0.00 2.78
30 31 4.020573 ACATGACTCGTTATCCAGGAAACA 60.021 41.667 0.00 0.00 0.00 2.83
31 32 4.610605 TGACTCGTTATCCAGGAAACAA 57.389 40.909 0.00 0.00 0.00 2.83
32 33 4.312443 TGACTCGTTATCCAGGAAACAAC 58.688 43.478 0.00 0.00 0.00 3.32
36 37 3.009695 TCGTTATCCAGGAAACAACCCAT 59.990 43.478 0.00 0.00 0.00 4.00
41 42 2.574369 TCCAGGAAACAACCCATACGAT 59.426 45.455 0.00 0.00 0.00 3.73
42 43 3.009695 TCCAGGAAACAACCCATACGATT 59.990 43.478 0.00 0.00 0.00 3.34
52 53 2.691409 CCATACGATTCTGTGTGGGT 57.309 50.000 12.95 0.00 44.68 4.51
56 57 5.123227 CCATACGATTCTGTGTGGGTAAAT 58.877 41.667 12.95 0.00 44.68 1.40
67 68 8.795842 TCTGTGTGGGTAAATATTAAAATCGT 57.204 30.769 0.00 0.00 0.00 3.73
108 109 3.256960 ATGGCCCACACGACCCTT 61.257 61.111 0.00 0.00 0.00 3.95
119 120 2.892334 CGACCCTTGTGTGGCAACG 61.892 63.158 0.00 0.00 42.51 4.10
129 130 1.863491 GTGGCAACGCGTGTAATCA 59.137 52.632 14.98 4.62 42.51 2.57
131 132 0.236187 TGGCAACGCGTGTAATCAAC 59.764 50.000 14.98 0.00 42.51 3.18
132 133 0.515564 GGCAACGCGTGTAATCAACT 59.484 50.000 14.98 0.00 0.00 3.16
133 134 1.069500 GGCAACGCGTGTAATCAACTT 60.069 47.619 14.98 0.00 0.00 2.66
134 135 2.603652 GGCAACGCGTGTAATCAACTTT 60.604 45.455 14.98 0.00 0.00 2.66
136 137 3.838550 GCAACGCGTGTAATCAACTTTAG 59.161 43.478 14.98 0.00 0.00 1.85
137 138 4.609783 GCAACGCGTGTAATCAACTTTAGT 60.610 41.667 14.98 0.00 0.00 2.24
138 139 5.437263 CAACGCGTGTAATCAACTTTAGTT 58.563 37.500 14.98 0.00 39.12 2.24
139 140 5.662211 ACGCGTGTAATCAACTTTAGTTT 57.338 34.783 12.93 0.00 35.83 2.66
140 141 6.051646 ACGCGTGTAATCAACTTTAGTTTT 57.948 33.333 12.93 0.00 35.83 2.43
143 144 6.849305 CGCGTGTAATCAACTTTAGTTTTTCT 59.151 34.615 0.00 0.00 35.83 2.52
144 145 7.149351 CGCGTGTAATCAACTTTAGTTTTTCTG 60.149 37.037 0.00 0.00 35.83 3.02
183 206 7.773224 TGCCATGTGTAATTAACTATAGTTGCT 59.227 33.333 25.27 13.01 38.90 3.91
305 331 3.058501 GCCGTGTGCAATTAACTAGTTGT 60.059 43.478 18.56 4.00 40.77 3.32
423 449 4.301072 AGTTGCCACATATACACACCTT 57.699 40.909 0.00 0.00 0.00 3.50
424 450 4.009675 AGTTGCCACATATACACACCTTG 58.990 43.478 0.00 0.00 0.00 3.61
587 617 0.968901 TTACGTGGCTCTCGACCCAT 60.969 55.000 0.00 0.00 32.95 4.00
598 628 0.908910 TCGACCCATATGGCAACTGT 59.091 50.000 16.97 8.27 37.83 3.55
600 630 1.401552 CGACCCATATGGCAACTGTTG 59.598 52.381 16.97 15.98 37.83 3.33
601 631 2.446435 GACCCATATGGCAACTGTTGT 58.554 47.619 20.57 5.98 37.83 3.32
612 642 6.832520 TGGCAACTGTTGTAATATTCATGT 57.167 33.333 20.57 0.00 37.61 3.21
634 666 6.761117 TGTAAATGAATCGAACGACATCAAG 58.239 36.000 14.86 0.00 30.59 3.02
648 680 1.039856 ATCAAGTGTGTTTGGGCCAC 58.960 50.000 5.23 0.00 0.00 5.01
660 692 0.466372 TGGGCCACGTTGAATTGTGA 60.466 50.000 0.00 0.00 38.36 3.58
716 748 4.863131 GTGACGAACACTAATCCTACTTGG 59.137 45.833 9.42 0.00 45.13 3.61
718 750 3.195661 CGAACACTAATCCTACTTGGCC 58.804 50.000 0.00 0.00 35.26 5.36
719 751 3.369052 CGAACACTAATCCTACTTGGCCA 60.369 47.826 0.00 0.00 35.26 5.36
722 754 4.040755 ACACTAATCCTACTTGGCCAGAT 58.959 43.478 5.11 1.33 35.26 2.90
740 772 4.142600 CCAGATGTTTAAGCCTCCTTTTCG 60.143 45.833 0.00 0.00 32.47 3.46
745 777 2.781681 TAAGCCTCCTTTTCGGAAGG 57.218 50.000 11.02 11.02 42.53 3.46
777 809 3.590643 TCCTACTCGGAGTTGGAGG 57.409 57.895 29.39 22.88 43.43 4.30
778 810 0.033405 TCCTACTCGGAGTTGGAGGG 60.033 60.000 29.39 17.51 43.43 4.30
779 811 0.033405 CCTACTCGGAGTTGGAGGGA 60.033 60.000 27.68 3.80 42.55 4.20
780 812 1.411787 CCTACTCGGAGTTGGAGGGAT 60.412 57.143 27.68 0.00 42.55 3.85
781 813 2.389715 CTACTCGGAGTTGGAGGGATT 58.610 52.381 16.95 0.00 35.82 3.01
782 814 0.905357 ACTCGGAGTTGGAGGGATTG 59.095 55.000 4.45 0.00 35.82 2.67
783 815 0.179000 CTCGGAGTTGGAGGGATTGG 59.821 60.000 0.00 0.00 0.00 3.16
784 816 1.224592 CGGAGTTGGAGGGATTGGG 59.775 63.158 0.00 0.00 0.00 4.12
785 817 1.562672 CGGAGTTGGAGGGATTGGGT 61.563 60.000 0.00 0.00 0.00 4.51
786 818 0.034089 GGAGTTGGAGGGATTGGGTG 60.034 60.000 0.00 0.00 0.00 4.61
787 819 0.991920 GAGTTGGAGGGATTGGGTGA 59.008 55.000 0.00 0.00 0.00 4.02
788 820 0.698818 AGTTGGAGGGATTGGGTGAC 59.301 55.000 0.00 0.00 0.00 3.67
789 821 0.676782 GTTGGAGGGATTGGGTGACG 60.677 60.000 0.00 0.00 0.00 4.35
790 822 0.838554 TTGGAGGGATTGGGTGACGA 60.839 55.000 0.00 0.00 0.00 4.20
791 823 0.838554 TGGAGGGATTGGGTGACGAA 60.839 55.000 0.00 0.00 0.00 3.85
815 847 3.632829 CGAATCCTACTCGGAGCTCGAA 61.633 54.545 7.83 0.00 46.38 3.71
816 848 5.665010 CGAATCCTACTCGGAGCTCGAAC 62.665 56.522 7.83 0.00 46.38 3.95
931 963 6.250739 CAGTCCATATAATGATGCGTACGTAC 59.749 42.308 17.90 15.90 0.00 3.67
932 964 5.514204 GTCCATATAATGATGCGTACGTACC 59.486 44.000 19.67 12.75 0.00 3.34
933 965 5.416639 TCCATATAATGATGCGTACGTACCT 59.583 40.000 19.67 5.03 0.00 3.08
934 966 6.598850 TCCATATAATGATGCGTACGTACCTA 59.401 38.462 19.67 9.37 0.00 3.08
948 981 6.183360 CGTACGTACCTATACCAAACTTACCA 60.183 42.308 19.67 0.00 0.00 3.25
952 1014 3.201487 ACCTATACCAAACTTACCAGCCC 59.799 47.826 0.00 0.00 0.00 5.19
1327 2007 1.344438 AGTGCTTCGACAAGACCATCA 59.656 47.619 0.00 0.00 0.00 3.07
1366 2046 0.988678 ACTCCAAGGGGATGGTAGCC 60.989 60.000 0.00 0.00 43.91 3.93
1477 2157 1.227556 CCTGCCACCATACGCTACC 60.228 63.158 0.00 0.00 0.00 3.18
1619 2299 2.181021 CCTCTACGACACGGTGGC 59.819 66.667 13.48 8.79 0.00 5.01
1627 2307 4.988598 ACACGGTGGCGAGCAAGG 62.989 66.667 13.48 0.00 0.00 3.61
1633 2313 2.125552 TGGCGAGCAAGGTCATCG 60.126 61.111 0.00 0.00 39.40 3.84
1900 2580 3.535629 CTCCACTGGCTGCGTTCCA 62.536 63.158 0.00 0.00 0.00 3.53
2052 2733 0.109342 AGGGCCTCAACAGTCTTGTG 59.891 55.000 0.00 0.00 37.67 3.33
2065 2746 1.838077 GTCTTGTGGGCTATAGGGTGT 59.162 52.381 1.04 0.00 0.00 4.16
2066 2747 3.036091 GTCTTGTGGGCTATAGGGTGTA 58.964 50.000 1.04 0.00 0.00 2.90
2067 2748 3.036091 TCTTGTGGGCTATAGGGTGTAC 58.964 50.000 1.04 0.00 0.00 2.90
2077 2758 5.258051 GCTATAGGGTGTACTAGATCTGCT 58.742 45.833 5.18 0.00 0.00 4.24
2108 2794 1.071605 GCTGCGACTTGTCCTGTAAG 58.928 55.000 0.00 0.00 0.00 2.34
2121 2808 4.196971 GTCCTGTAAGTTGGAAGTGTTGT 58.803 43.478 0.00 0.00 33.72 3.32
2122 2809 5.104859 TGTCCTGTAAGTTGGAAGTGTTGTA 60.105 40.000 0.00 0.00 33.72 2.41
2123 2810 5.235831 GTCCTGTAAGTTGGAAGTGTTGTAC 59.764 44.000 0.00 0.00 33.72 2.90
2124 2811 5.129815 TCCTGTAAGTTGGAAGTGTTGTACT 59.870 40.000 0.00 0.00 42.89 2.73
2125 2812 5.465724 CCTGTAAGTTGGAAGTGTTGTACTC 59.534 44.000 0.00 0.00 39.18 2.59
2126 2813 5.362263 TGTAAGTTGGAAGTGTTGTACTCC 58.638 41.667 0.00 0.00 39.18 3.85
2220 2915 4.095632 TGTTCGCTCTGTTGAATTGAACAA 59.904 37.500 11.66 2.94 40.63 2.83
2222 2917 5.242069 TCGCTCTGTTGAATTGAACAAAA 57.758 34.783 11.66 2.71 35.44 2.44
2224 2919 4.442073 CGCTCTGTTGAATTGAACAAAAGG 59.558 41.667 11.66 0.68 35.44 3.11
2227 2922 6.145048 GCTCTGTTGAATTGAACAAAAGGATG 59.855 38.462 11.66 0.00 35.44 3.51
2228 2923 6.514947 TCTGTTGAATTGAACAAAAGGATGG 58.485 36.000 11.66 0.00 35.44 3.51
2229 2924 6.323482 TCTGTTGAATTGAACAAAAGGATGGA 59.677 34.615 11.66 0.66 35.44 3.41
2230 2925 6.279882 TGTTGAATTGAACAAAAGGATGGAC 58.720 36.000 8.09 0.00 32.84 4.02
2231 2926 5.467035 TGAATTGAACAAAAGGATGGACC 57.533 39.130 0.00 0.00 39.35 4.46
2232 2927 4.022416 TGAATTGAACAAAAGGATGGACCG 60.022 41.667 0.00 0.00 44.74 4.79
2233 2928 2.940994 TGAACAAAAGGATGGACCGA 57.059 45.000 0.00 0.00 44.74 4.69
2234 2929 2.778299 TGAACAAAAGGATGGACCGAG 58.222 47.619 0.00 0.00 44.74 4.63
2238 3203 3.146847 ACAAAAGGATGGACCGAGAAAC 58.853 45.455 0.00 0.00 44.74 2.78
2239 3204 3.146066 CAAAAGGATGGACCGAGAAACA 58.854 45.455 0.00 0.00 44.74 2.83
2269 3246 3.007831 AGAAAAGGGCAACTCTCTCTCTG 59.992 47.826 0.00 0.00 0.00 3.35
2344 3322 3.530265 TCTTCACTGTGTACGTTGGTT 57.470 42.857 7.79 0.00 0.00 3.67
2350 3328 6.680874 TCACTGTGTACGTTGGTTAAAAAT 57.319 33.333 7.79 0.00 0.00 1.82
2397 3375 9.887406 AAAATATAAACGTGTACTTCCAAGTTG 57.113 29.630 0.00 0.00 40.37 3.16
2399 3377 9.709495 AATATAAACGTGTACTTCCAAGTTGTA 57.291 29.630 1.45 0.00 40.37 2.41
2400 3378 9.709495 ATATAAACGTGTACTTCCAAGTTGTAA 57.291 29.630 1.45 0.00 40.37 2.41
2414 3392 7.390823 TCCAAGTTGTAACATGCTCAATACTA 58.609 34.615 1.45 0.00 0.00 1.82
2415 3393 7.333423 TCCAAGTTGTAACATGCTCAATACTAC 59.667 37.037 1.45 0.00 0.00 2.73
2460 3453 3.084786 CCAACTTCCATTCCAAGGAGAC 58.915 50.000 0.00 0.00 36.33 3.36
2527 3555 1.476891 GACCATTACAGGAGAGCACGA 59.523 52.381 0.00 0.00 0.00 4.35
2532 3560 0.680280 TACAGGAGAGCACGAGACCC 60.680 60.000 0.00 0.00 0.00 4.46
2533 3561 1.979155 CAGGAGAGCACGAGACCCA 60.979 63.158 0.00 0.00 0.00 4.51
2535 3563 1.979693 GGAGAGCACGAGACCCACT 60.980 63.158 0.00 0.00 0.00 4.00
2536 3564 1.214062 GAGAGCACGAGACCCACTG 59.786 63.158 0.00 0.00 0.00 3.66
2537 3565 2.433318 GAGCACGAGACCCACTGC 60.433 66.667 0.00 0.00 0.00 4.40
2538 3566 4.363990 AGCACGAGACCCACTGCG 62.364 66.667 0.00 0.00 0.00 5.18
2539 3567 4.664677 GCACGAGACCCACTGCGT 62.665 66.667 0.00 0.00 34.60 5.24
2540 3568 2.734723 CACGAGACCCACTGCGTG 60.735 66.667 0.00 0.00 40.51 5.34
2541 3569 2.910479 ACGAGACCCACTGCGTGA 60.910 61.111 9.75 0.00 35.23 4.35
2591 3628 4.461081 ACCAGAACTAAACAACAGCAAACA 59.539 37.500 0.00 0.00 0.00 2.83
2667 3750 2.348666 ACGAGATTGTAATCAGCAACGC 59.651 45.455 7.30 0.00 37.89 4.84
2842 3926 5.528690 TGGCAAATATCTGCATCTTCTGTAC 59.471 40.000 2.94 0.00 44.52 2.90
2863 3947 0.980423 AGGGACTGTTTCTCCAGCTC 59.020 55.000 0.00 0.00 37.18 4.09
2903 3992 4.092091 GTCAGTGCATTCTTCGAAGTAAGG 59.908 45.833 23.85 17.96 0.00 2.69
2909 3998 1.079405 CTTCGAAGTAAGGGCGGCA 60.079 57.895 17.24 0.00 0.00 5.69
3013 4106 4.141824 ACAAGCTAGATTACCTCCTGCTTC 60.142 45.833 0.00 0.00 39.42 3.86
3036 4129 3.491619 CCGACAGTAATGTCCATCTCCAG 60.492 52.174 17.05 1.17 35.52 3.86
3043 4136 6.267699 CAGTAATGTCCATCTCCAGTACCATA 59.732 42.308 0.00 0.00 33.79 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 3.369471 CCTGGATAACGAGTCATGTGGTT 60.369 47.826 0.00 0.00 0.00 3.67
5 6 2.430694 TCCTGGATAACGAGTCATGTGG 59.569 50.000 0.00 0.00 0.00 4.17
6 7 3.801114 TCCTGGATAACGAGTCATGTG 57.199 47.619 0.00 0.00 0.00 3.21
7 8 4.020573 TGTTTCCTGGATAACGAGTCATGT 60.021 41.667 0.00 0.00 0.00 3.21
8 9 4.503910 TGTTTCCTGGATAACGAGTCATG 58.496 43.478 0.00 0.00 0.00 3.07
9 10 4.819105 TGTTTCCTGGATAACGAGTCAT 57.181 40.909 0.00 0.00 0.00 3.06
10 11 4.312443 GTTGTTTCCTGGATAACGAGTCA 58.688 43.478 0.00 0.00 0.00 3.41
11 12 3.683340 GGTTGTTTCCTGGATAACGAGTC 59.317 47.826 0.00 0.00 0.00 3.36
12 13 3.558533 GGGTTGTTTCCTGGATAACGAGT 60.559 47.826 0.00 0.00 0.00 4.18
13 14 3.007635 GGGTTGTTTCCTGGATAACGAG 58.992 50.000 0.00 0.00 0.00 4.18
14 15 2.372504 TGGGTTGTTTCCTGGATAACGA 59.627 45.455 0.00 2.69 0.00 3.85
15 16 2.785562 TGGGTTGTTTCCTGGATAACG 58.214 47.619 0.00 0.00 0.00 3.18
16 17 4.334481 CGTATGGGTTGTTTCCTGGATAAC 59.666 45.833 0.00 6.06 0.00 1.89
17 18 4.225492 TCGTATGGGTTGTTTCCTGGATAA 59.775 41.667 0.00 0.00 0.00 1.75
18 19 3.775866 TCGTATGGGTTGTTTCCTGGATA 59.224 43.478 0.00 0.00 0.00 2.59
19 20 2.574369 TCGTATGGGTTGTTTCCTGGAT 59.426 45.455 0.00 0.00 0.00 3.41
20 21 1.979308 TCGTATGGGTTGTTTCCTGGA 59.021 47.619 0.00 0.00 0.00 3.86
21 22 2.483014 TCGTATGGGTTGTTTCCTGG 57.517 50.000 0.00 0.00 0.00 4.45
22 23 4.094887 CAGAATCGTATGGGTTGTTTCCTG 59.905 45.833 0.00 0.00 0.00 3.86
23 24 4.261801 CAGAATCGTATGGGTTGTTTCCT 58.738 43.478 0.00 0.00 0.00 3.36
24 25 4.007659 ACAGAATCGTATGGGTTGTTTCC 58.992 43.478 0.00 0.00 0.00 3.13
25 26 4.454504 ACACAGAATCGTATGGGTTGTTTC 59.545 41.667 0.00 0.00 23.59 2.78
26 27 4.215399 CACACAGAATCGTATGGGTTGTTT 59.785 41.667 0.00 0.00 27.17 2.83
27 28 3.751175 CACACAGAATCGTATGGGTTGTT 59.249 43.478 0.00 0.00 27.17 2.83
28 29 3.334691 CACACAGAATCGTATGGGTTGT 58.665 45.455 0.00 0.00 27.17 3.32
29 30 2.677836 CCACACAGAATCGTATGGGTTG 59.322 50.000 0.00 0.00 27.17 3.77
30 31 2.355716 CCCACACAGAATCGTATGGGTT 60.356 50.000 11.57 0.00 41.67 4.11
31 32 1.209504 CCCACACAGAATCGTATGGGT 59.790 52.381 11.57 0.00 41.67 4.51
32 33 1.953559 CCCACACAGAATCGTATGGG 58.046 55.000 7.07 7.07 40.87 4.00
36 37 9.887629 TTTAATATTTACCCACACAGAATCGTA 57.112 29.630 0.00 0.00 0.00 3.43
41 42 9.233649 ACGATTTTAATATTTACCCACACAGAA 57.766 29.630 0.00 0.00 0.00 3.02
42 43 8.795842 ACGATTTTAATATTTACCCACACAGA 57.204 30.769 0.00 0.00 0.00 3.41
56 57 7.466185 CGCCTAAATGTGTGGACGATTTTAATA 60.466 37.037 0.00 0.00 0.00 0.98
65 66 1.295357 TGCGCCTAAATGTGTGGACG 61.295 55.000 4.18 0.00 0.00 4.79
67 68 1.305219 GCTGCGCCTAAATGTGTGGA 61.305 55.000 4.18 0.00 0.00 4.02
78 79 4.899239 GCCATCGTAGCTGCGCCT 62.899 66.667 20.12 6.31 0.00 5.52
108 109 1.160946 ATTACACGCGTTGCCACACA 61.161 50.000 10.22 0.00 0.00 3.72
119 120 7.853929 TCAGAAAAACTAAAGTTGATTACACGC 59.146 33.333 0.00 0.00 38.44 5.34
120 121 9.878599 ATCAGAAAAACTAAAGTTGATTACACG 57.121 29.630 0.00 0.00 38.44 4.49
386 412 5.808540 GTGGCAACTACTTAATCACATACGA 59.191 40.000 0.00 0.00 37.61 3.43
415 441 1.143684 AGATGGCAACTCAAGGTGTGT 59.856 47.619 0.00 0.00 37.61 3.72
423 449 3.200605 ACATGGTGATAGATGGCAACTCA 59.799 43.478 0.00 0.00 37.61 3.41
424 450 3.562973 CACATGGTGATAGATGGCAACTC 59.437 47.826 0.00 0.00 35.23 3.01
500 529 3.774959 CTCCTCGCCCGAATGGACG 62.775 68.421 0.00 0.00 37.49 4.79
587 617 8.518430 ACATGAATATTACAACAGTTGCCATA 57.482 30.769 13.56 9.86 0.00 2.74
612 642 6.367695 ACACTTGATGTCGTTCGATTCATTTA 59.632 34.615 10.05 0.00 36.54 1.40
618 649 3.390135 ACACACTTGATGTCGTTCGATT 58.610 40.909 0.00 0.00 40.64 3.34
634 666 1.226831 CAACGTGGCCCAAACACAC 60.227 57.895 0.00 0.00 38.74 3.82
648 680 2.222931 ACACGTGTGTCACAATTCAACG 60.223 45.455 22.71 8.47 40.24 4.10
672 704 8.392612 CGTCACCAAATAATATTCCTAAAACGT 58.607 33.333 0.00 0.00 0.00 3.99
677 709 8.885722 GTGTTCGTCACCAAATAATATTCCTAA 58.114 33.333 0.00 0.00 40.84 2.69
678 710 8.428186 GTGTTCGTCACCAAATAATATTCCTA 57.572 34.615 0.00 0.00 40.84 2.94
679 711 7.316544 GTGTTCGTCACCAAATAATATTCCT 57.683 36.000 0.00 0.00 40.84 3.36
716 748 2.426842 AGGAGGCTTAAACATCTGGC 57.573 50.000 0.00 0.00 0.00 4.85
718 750 4.142600 CCGAAAAGGAGGCTTAAACATCTG 60.143 45.833 0.00 0.00 45.00 2.90
719 751 4.010349 CCGAAAAGGAGGCTTAAACATCT 58.990 43.478 0.00 0.00 45.00 2.90
722 754 3.495434 TCCGAAAAGGAGGCTTAAACA 57.505 42.857 0.00 0.00 45.98 2.83
760 792 0.033405 TCCCTCCAACTCCGAGTAGG 60.033 60.000 0.26 5.21 42.97 3.18
761 793 2.074729 ATCCCTCCAACTCCGAGTAG 57.925 55.000 0.26 0.00 0.00 2.57
762 794 2.108168 CAATCCCTCCAACTCCGAGTA 58.892 52.381 0.26 0.00 0.00 2.59
763 795 0.905357 CAATCCCTCCAACTCCGAGT 59.095 55.000 0.00 0.00 0.00 4.18
764 796 0.179000 CCAATCCCTCCAACTCCGAG 59.821 60.000 0.00 0.00 0.00 4.63
765 797 1.271840 CCCAATCCCTCCAACTCCGA 61.272 60.000 0.00 0.00 0.00 4.55
766 798 1.224592 CCCAATCCCTCCAACTCCG 59.775 63.158 0.00 0.00 0.00 4.63
767 799 0.034089 CACCCAATCCCTCCAACTCC 60.034 60.000 0.00 0.00 0.00 3.85
768 800 0.991920 TCACCCAATCCCTCCAACTC 59.008 55.000 0.00 0.00 0.00 3.01
769 801 0.698818 GTCACCCAATCCCTCCAACT 59.301 55.000 0.00 0.00 0.00 3.16
770 802 0.676782 CGTCACCCAATCCCTCCAAC 60.677 60.000 0.00 0.00 0.00 3.77
771 803 0.838554 TCGTCACCCAATCCCTCCAA 60.839 55.000 0.00 0.00 0.00 3.53
772 804 0.838554 TTCGTCACCCAATCCCTCCA 60.839 55.000 0.00 0.00 0.00 3.86
773 805 0.392595 GTTCGTCACCCAATCCCTCC 60.393 60.000 0.00 0.00 0.00 4.30
774 806 0.323629 TGTTCGTCACCCAATCCCTC 59.676 55.000 0.00 0.00 0.00 4.30
775 807 0.036306 GTGTTCGTCACCCAATCCCT 59.964 55.000 3.00 0.00 40.84 4.20
776 808 1.296056 CGTGTTCGTCACCCAATCCC 61.296 60.000 7.61 0.00 43.51 3.85
777 809 0.320073 TCGTGTTCGTCACCCAATCC 60.320 55.000 7.61 0.00 43.51 3.01
778 810 1.504359 TTCGTGTTCGTCACCCAATC 58.496 50.000 7.61 0.00 43.51 2.67
779 811 2.073816 GATTCGTGTTCGTCACCCAAT 58.926 47.619 7.61 6.52 43.51 3.16
780 812 1.504359 GATTCGTGTTCGTCACCCAA 58.496 50.000 7.61 2.95 43.51 4.12
781 813 0.320073 GGATTCGTGTTCGTCACCCA 60.320 55.000 7.61 0.00 43.51 4.51
782 814 0.037605 AGGATTCGTGTTCGTCACCC 60.038 55.000 7.61 4.16 43.51 4.61
783 815 2.094854 AGTAGGATTCGTGTTCGTCACC 60.095 50.000 7.61 0.00 43.51 4.02
784 816 3.169733 GAGTAGGATTCGTGTTCGTCAC 58.830 50.000 4.07 4.07 43.03 3.67
785 817 2.159612 CGAGTAGGATTCGTGTTCGTCA 60.160 50.000 6.32 0.00 38.33 4.35
786 818 2.438583 CGAGTAGGATTCGTGTTCGTC 58.561 52.381 6.32 0.00 38.33 4.20
787 819 1.131883 CCGAGTAGGATTCGTGTTCGT 59.868 52.381 10.98 0.00 45.00 3.85
788 820 1.399440 TCCGAGTAGGATTCGTGTTCG 59.601 52.381 0.00 7.11 45.98 3.95
815 847 2.908817 GTGTTCGTCACCCAATCGT 58.091 52.632 3.00 0.00 40.84 3.73
907 939 5.386958 ACGTACGCATCATTATATGGACT 57.613 39.130 16.72 0.00 0.00 3.85
931 963 3.743269 CGGGCTGGTAAGTTTGGTATAGG 60.743 52.174 0.00 0.00 0.00 2.57
932 964 3.118519 ACGGGCTGGTAAGTTTGGTATAG 60.119 47.826 0.00 0.00 0.00 1.31
933 965 2.839425 ACGGGCTGGTAAGTTTGGTATA 59.161 45.455 0.00 0.00 0.00 1.47
934 966 1.631898 ACGGGCTGGTAAGTTTGGTAT 59.368 47.619 0.00 0.00 0.00 2.73
948 981 2.425668 CCGAATTTATTGGAAACGGGCT 59.574 45.455 0.00 0.00 36.08 5.19
952 1014 5.387958 GCAAACACCGAATTTATTGGAAACG 60.388 40.000 0.00 0.00 0.00 3.60
1247 1927 2.572284 GGGACCACTCGTCTTCGG 59.428 66.667 0.00 0.00 41.64 4.30
1275 1955 1.329599 GACAACGCTCGTGAAAGGTTT 59.670 47.619 0.00 0.00 0.00 3.27
1327 2007 2.437359 GAGCGAATGCAGCAGGGT 60.437 61.111 0.00 0.00 46.23 4.34
1477 2157 0.378962 GTGATCACCTCCTCGACGAG 59.621 60.000 18.08 18.08 0.00 4.18
1619 2299 2.892425 GGGCGATGACCTTGCTCG 60.892 66.667 0.00 0.00 34.36 5.03
1820 2500 4.002506 TCACCATGTCCTGCGCGT 62.003 61.111 8.43 0.00 0.00 6.01
1821 2501 3.490759 GTCACCATGTCCTGCGCG 61.491 66.667 0.00 0.00 0.00 6.86
2012 2693 0.025001 CGTTTCACGATCGACCATGC 59.975 55.000 24.34 6.22 46.05 4.06
2037 2718 0.109342 AGCCCACAAGACTGTTGAGG 59.891 55.000 0.00 0.00 31.64 3.86
2052 2733 4.951094 CAGATCTAGTACACCCTATAGCCC 59.049 50.000 0.00 0.00 0.00 5.19
2065 2746 3.825143 TGCATGCAAGCAGATCTAGTA 57.175 42.857 20.30 0.00 40.11 1.82
2066 2747 2.704464 TGCATGCAAGCAGATCTAGT 57.296 45.000 20.30 0.00 40.11 2.57
2096 2782 4.451900 ACACTTCCAACTTACAGGACAAG 58.548 43.478 0.00 0.00 32.62 3.16
2108 2794 4.392138 GCATAGGAGTACAACACTTCCAAC 59.608 45.833 0.00 0.00 37.72 3.77
2121 2808 5.392703 CGTCAACAACTGTAGCATAGGAGTA 60.393 44.000 0.00 0.00 0.00 2.59
2122 2809 4.618460 CGTCAACAACTGTAGCATAGGAGT 60.618 45.833 0.00 0.00 0.00 3.85
2123 2810 3.859961 CGTCAACAACTGTAGCATAGGAG 59.140 47.826 0.00 0.00 0.00 3.69
2124 2811 3.845178 CGTCAACAACTGTAGCATAGGA 58.155 45.455 0.00 0.00 0.00 2.94
2125 2812 2.348666 GCGTCAACAACTGTAGCATAGG 59.651 50.000 0.00 0.00 0.00 2.57
2126 2813 3.254060 AGCGTCAACAACTGTAGCATAG 58.746 45.455 0.00 0.00 33.20 2.23
2188 2883 2.693069 ACAGAGCGAACAGATCCTTTG 58.307 47.619 0.00 0.00 35.47 2.77
2198 2893 4.209452 TGTTCAATTCAACAGAGCGAAC 57.791 40.909 0.00 0.00 32.36 3.95
2220 2915 3.502123 TTGTTTCTCGGTCCATCCTTT 57.498 42.857 0.00 0.00 0.00 3.11
2222 2917 3.502123 TTTTGTTTCTCGGTCCATCCT 57.498 42.857 0.00 0.00 0.00 3.24
2224 2919 5.768317 TGAATTTTTGTTTCTCGGTCCATC 58.232 37.500 0.00 0.00 0.00 3.51
2227 2922 5.432885 TCTGAATTTTTGTTTCTCGGTCC 57.567 39.130 0.00 0.00 0.00 4.46
2228 2923 7.043391 CCTTTTCTGAATTTTTGTTTCTCGGTC 60.043 37.037 0.00 0.00 0.00 4.79
2229 2924 6.756542 CCTTTTCTGAATTTTTGTTTCTCGGT 59.243 34.615 0.00 0.00 0.00 4.69
2230 2925 6.200854 CCCTTTTCTGAATTTTTGTTTCTCGG 59.799 38.462 0.00 0.00 0.00 4.63
2231 2926 6.292328 GCCCTTTTCTGAATTTTTGTTTCTCG 60.292 38.462 0.00 0.00 0.00 4.04
2232 2927 6.538381 TGCCCTTTTCTGAATTTTTGTTTCTC 59.462 34.615 0.00 0.00 0.00 2.87
2233 2928 6.413892 TGCCCTTTTCTGAATTTTTGTTTCT 58.586 32.000 0.00 0.00 0.00 2.52
2234 2929 6.676237 TGCCCTTTTCTGAATTTTTGTTTC 57.324 33.333 0.00 0.00 0.00 2.78
2238 3203 6.051074 AGAGTTGCCCTTTTCTGAATTTTTG 58.949 36.000 0.00 0.00 0.00 2.44
2239 3204 6.098838 AGAGAGTTGCCCTTTTCTGAATTTTT 59.901 34.615 0.00 0.00 0.00 1.94
2269 3246 7.867445 TCTTGTGAACACTGAAAAAGAAAAC 57.133 32.000 6.51 0.00 0.00 2.43
2330 3308 9.537848 GAGATTATTTTTAACCAACGTACACAG 57.462 33.333 0.00 0.00 0.00 3.66
2383 3361 5.373222 AGCATGTTACAACTTGGAAGTACA 58.627 37.500 9.28 0.00 38.57 2.90
2386 3364 4.460263 TGAGCATGTTACAACTTGGAAGT 58.540 39.130 9.28 0.00 42.04 3.01
2387 3365 5.437289 TTGAGCATGTTACAACTTGGAAG 57.563 39.130 9.28 0.00 35.36 3.46
2388 3366 6.714810 AGTATTGAGCATGTTACAACTTGGAA 59.285 34.615 9.28 0.00 35.36 3.53
2389 3367 6.237901 AGTATTGAGCATGTTACAACTTGGA 58.762 36.000 9.28 0.00 35.36 3.53
2390 3368 6.500684 AGTATTGAGCATGTTACAACTTGG 57.499 37.500 9.28 0.00 35.36 3.61
2391 3369 8.028540 TGTAGTATTGAGCATGTTACAACTTG 57.971 34.615 0.00 4.15 37.19 3.16
2392 3370 8.615878 TTGTAGTATTGAGCATGTTACAACTT 57.384 30.769 0.00 0.00 0.00 2.66
2393 3371 8.792830 ATTGTAGTATTGAGCATGTTACAACT 57.207 30.769 0.00 0.00 32.36 3.16
2397 3375 9.708222 CTGAAATTGTAGTATTGAGCATGTTAC 57.292 33.333 0.00 0.00 0.00 2.50
2399 3377 7.121759 AGCTGAAATTGTAGTATTGAGCATGTT 59.878 33.333 0.00 0.00 31.18 2.71
2400 3378 6.600822 AGCTGAAATTGTAGTATTGAGCATGT 59.399 34.615 0.00 0.00 31.18 3.21
2414 3392 5.537674 ACATGGAGAAAAGAGCTGAAATTGT 59.462 36.000 0.00 0.00 0.00 2.71
2415 3393 6.022163 ACATGGAGAAAAGAGCTGAAATTG 57.978 37.500 0.00 0.00 0.00 2.32
2460 3453 0.512952 CTTGAACTTTCGTGGAGGCG 59.487 55.000 0.00 0.00 0.00 5.52
2467 3460 3.938963 TGCTCAGAAACTTGAACTTTCGT 59.061 39.130 0.00 0.00 33.56 3.85
2533 3561 4.517453 TGGCTTTATTTAAGTTCACGCAGT 59.483 37.500 0.00 0.00 37.44 4.40
2535 3563 5.440234 TTGGCTTTATTTAAGTTCACGCA 57.560 34.783 0.00 0.00 36.19 5.24
2536 3564 6.757026 TTTTGGCTTTATTTAAGTTCACGC 57.243 33.333 0.00 0.00 36.19 5.34
2564 3601 4.814234 TGCTGTTGTTTAGTTCTGGTAGTG 59.186 41.667 0.00 0.00 0.00 2.74
2591 3628 5.821470 CAGGAAGTGATTGATAATGCAGTCT 59.179 40.000 0.00 0.00 0.00 3.24
2667 3750 7.271511 AGCAGATATCTTAAAGACTTGTCCAG 58.728 38.462 1.33 0.00 0.00 3.86
2842 3926 1.072965 AGCTGGAGAAACAGTCCCTTG 59.927 52.381 0.00 0.00 40.59 3.61
2863 3947 2.131972 TGACCGAAGTGTTCATTGACG 58.868 47.619 0.00 0.00 0.00 4.35
2960 4049 9.454859 TTGATTAAATTCACTTTTTGTTGGGTT 57.545 25.926 0.00 0.00 0.00 4.11
3036 4129 4.228824 TGGGAGGTACAAGGATATGGTAC 58.771 47.826 0.00 0.00 37.30 3.34
3043 4136 1.080498 TGGTCTGGGAGGTACAAGGAT 59.920 52.381 0.00 0.00 0.00 3.24


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

AutoCloner maintained by Alex Coulton.