Multiple sequence alignment - TraesCS4B01G394700

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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 TraesCS4B01G394700 chr4B 100.000 3077 0 0 1 3077 668872284 668875360 0.000000e+00 5683.0
1 TraesCS4B01G394700 chr4B 83.058 242 23 8 2251 2481 508821784 508821550 1.450000e-48 204.0
2 TraesCS4B01G394700 chr5A 92.590 1309 66 18 788 2086 708182846 708184133 0.000000e+00 1851.0
3 TraesCS4B01G394700 chr5A 98.867 706 7 1 1 706 513703990 513703286 0.000000e+00 1258.0
4 TraesCS4B01G394700 chrUn 91.684 950 46 14 1258 2197 28781714 28782640 0.000000e+00 1286.0
5 TraesCS4B01G394700 chrUn 94.634 205 11 0 986 1190 28781489 28781693 4.950000e-83 318.0
6 TraesCS4B01G394700 chrUn 90.000 60 5 1 2266 2325 47673020 47673078 3.290000e-10 76.8
7 TraesCS4B01G394700 chrUn 93.182 44 0 3 739 782 28781436 28781476 9.210000e-06 62.1
8 TraesCS4B01G394700 chrUn 100.000 29 0 0 2213 2241 50582737 50582709 2.000000e-03 54.7
9 TraesCS4B01G394700 chrUn 96.875 32 1 0 2210 2241 278343309 278343340 2.000000e-03 54.7
10 TraesCS4B01G394700 chrUn 96.875 32 1 0 2210 2241 278350586 278350617 2.000000e-03 54.7
11 TraesCS4B01G394700 chrUn 100.000 29 0 0 2213 2241 325541600 325541572 2.000000e-03 54.7
12 TraesCS4B01G394700 chr7B 94.909 825 32 5 2257 3077 627071641 627070823 0.000000e+00 1282.0
13 TraesCS4B01G394700 chr7B 99.000 700 7 0 1 700 616406850 616406151 0.000000e+00 1254.0
14 TraesCS4B01G394700 chr7B 98.718 702 9 0 1 702 720550978 720551679 0.000000e+00 1247.0
15 TraesCS4B01G394700 chr7B 83.564 1083 144 18 1001 2078 597453388 597454441 0.000000e+00 983.0
16 TraesCS4B01G394700 chr7B 86.808 614 53 12 2476 3075 173870539 173869940 0.000000e+00 660.0
17 TraesCS4B01G394700 chr3A 99.153 708 5 1 1 707 12636588 12637295 0.000000e+00 1273.0
18 TraesCS4B01G394700 chr3A 77.500 1040 160 50 1001 2009 663441806 663440810 9.640000e-155 556.0
19 TraesCS4B01G394700 chr5B 99.429 700 4 0 1 700 484825525 484826224 0.000000e+00 1271.0
20 TraesCS4B01G394700 chr5B 78.257 998 136 46 1010 1970 710608524 710609477 1.600000e-157 566.0
21 TraesCS4B01G394700 chr5B 76.591 974 152 49 1010 1957 711858985 711858062 1.670000e-127 466.0
22 TraesCS4B01G394700 chr5B 74.952 1042 207 23 1010 2042 710593180 710594176 2.190000e-116 429.0
23 TraesCS4B01G394700 chr3B 99.286 700 5 0 1 700 809184280 809183581 0.000000e+00 1266.0
24 TraesCS4B01G394700 chr3B 83.051 236 22 8 2257 2481 555087618 555087390 6.730000e-47 198.0
25 TraesCS4B01G394700 chr3B 100.000 28 0 0 2214 2241 5945484 5945511 6.000000e-03 52.8
26 TraesCS4B01G394700 chr3B 100.000 28 0 0 2214 2241 658489667 658489640 6.000000e-03 52.8
27 TraesCS4B01G394700 chr6A 99.000 700 7 0 1 700 3635537 3636236 0.000000e+00 1254.0
28 TraesCS4B01G394700 chr6A 91.787 828 61 2 2255 3077 213835987 213835162 0.000000e+00 1146.0
29 TraesCS4B01G394700 chr6A 85.809 606 62 16 2471 3063 45067311 45066717 3.370000e-174 621.0
30 TraesCS4B01G394700 chr6A 85.321 109 13 3 2265 2371 256470715 256470822 3.240000e-20 110.0
31 TraesCS4B01G394700 chr4A 99.000 700 6 1 1 700 741027559 741028257 0.000000e+00 1253.0
32 TraesCS4B01G394700 chr4A 77.083 1056 164 49 1013 2032 604105189 604104176 3.490000e-149 538.0
33 TraesCS4B01G394700 chr4A 77.213 983 144 48 1009 1956 663696135 663695198 4.580000e-138 501.0
34 TraesCS4B01G394700 chr4A 85.417 96 13 1 2257 2352 665729165 665729071 7.020000e-17 99.0
35 TraesCS4B01G394700 chr4A 100.000 28 0 0 2214 2241 68697288 68697261 6.000000e-03 52.8
36 TraesCS4B01G394700 chr2A 98.857 700 8 0 1 700 750961166 750961865 0.000000e+00 1249.0
37 TraesCS4B01G394700 chr2A 77.534 957 128 45 1030 1956 15959827 15960726 2.130000e-136 496.0
38 TraesCS4B01G394700 chr2A 76.105 950 156 49 1030 1951 15756477 15757383 6.100000e-117 431.0
39 TraesCS4B01G394700 chr7A 84.051 1091 140 21 1001 2086 637994380 637995441 0.000000e+00 1020.0
40 TraesCS4B01G394700 chr7A 81.118 1091 142 32 1001 2081 638132174 638133210 0.000000e+00 815.0
41 TraesCS4B01G394700 chr7A 76.829 984 147 46 1009 1956 51662508 51661570 2.150000e-131 479.0
42 TraesCS4B01G394700 chr7D 83.776 1091 143 18 1001 2086 552325048 552326109 0.000000e+00 1003.0
43 TraesCS4B01G394700 chr7D 85.965 57 6 2 2719 2773 537239891 537239835 3.310000e-05 60.2
44 TraesCS4B01G394700 chr1A 88.875 818 63 7 2256 3068 440683192 440683986 0.000000e+00 981.0
45 TraesCS4B01G394700 chr1A 74.724 906 170 44 1002 1899 71784572 71785426 1.760000e-92 350.0
46 TraesCS4B01G394700 chr1A 83.051 236 22 8 2258 2481 99001321 99001092 6.730000e-47 198.0
47 TraesCS4B01G394700 chr5D 79.861 1008 156 28 1034 2031 558956952 558955982 0.000000e+00 693.0
48 TraesCS4B01G394700 chr5D 77.259 985 130 55 1010 1966 560224906 560225824 2.760000e-135 492.0
49 TraesCS4B01G394700 chr1B 87.134 614 55 11 2476 3075 108839264 108839867 0.000000e+00 675.0
50 TraesCS4B01G394700 chr2B 86.058 624 53 14 2476 3075 73270666 73270053 9.300000e-180 640.0
51 TraesCS4B01G394700 chr2B 94.444 54 3 0 2715 2768 161149711 161149658 1.970000e-12 84.2
52 TraesCS4B01G394700 chr1D 76.084 761 135 35 1006 1759 72497923 72498643 1.360000e-93 353.0
53 TraesCS4B01G394700 chr6D 88.889 45 4 1 2214 2257 62426637 62426593 2.000000e-03 54.7


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 TraesCS4B01G394700 chr4B 668872284 668875360 3076 False 5683.000000 5683 100.000000 1 3077 1 chr4B.!!$F1 3076
1 TraesCS4B01G394700 chr5A 708182846 708184133 1287 False 1851.000000 1851 92.590000 788 2086 1 chr5A.!!$F1 1298
2 TraesCS4B01G394700 chr5A 513703286 513703990 704 True 1258.000000 1258 98.867000 1 706 1 chr5A.!!$R1 705
3 TraesCS4B01G394700 chrUn 28781436 28782640 1204 False 555.366667 1286 93.166667 739 2197 3 chrUn.!!$F4 1458
4 TraesCS4B01G394700 chr7B 627070823 627071641 818 True 1282.000000 1282 94.909000 2257 3077 1 chr7B.!!$R3 820
5 TraesCS4B01G394700 chr7B 616406151 616406850 699 True 1254.000000 1254 99.000000 1 700 1 chr7B.!!$R2 699
6 TraesCS4B01G394700 chr7B 720550978 720551679 701 False 1247.000000 1247 98.718000 1 702 1 chr7B.!!$F2 701
7 TraesCS4B01G394700 chr7B 597453388 597454441 1053 False 983.000000 983 83.564000 1001 2078 1 chr7B.!!$F1 1077
8 TraesCS4B01G394700 chr7B 173869940 173870539 599 True 660.000000 660 86.808000 2476 3075 1 chr7B.!!$R1 599
9 TraesCS4B01G394700 chr3A 12636588 12637295 707 False 1273.000000 1273 99.153000 1 707 1 chr3A.!!$F1 706
10 TraesCS4B01G394700 chr3A 663440810 663441806 996 True 556.000000 556 77.500000 1001 2009 1 chr3A.!!$R1 1008
11 TraesCS4B01G394700 chr5B 484825525 484826224 699 False 1271.000000 1271 99.429000 1 700 1 chr5B.!!$F1 699
12 TraesCS4B01G394700 chr5B 710608524 710609477 953 False 566.000000 566 78.257000 1010 1970 1 chr5B.!!$F3 960
13 TraesCS4B01G394700 chr5B 711858062 711858985 923 True 466.000000 466 76.591000 1010 1957 1 chr5B.!!$R1 947
14 TraesCS4B01G394700 chr5B 710593180 710594176 996 False 429.000000 429 74.952000 1010 2042 1 chr5B.!!$F2 1032
15 TraesCS4B01G394700 chr3B 809183581 809184280 699 True 1266.000000 1266 99.286000 1 700 1 chr3B.!!$R3 699
16 TraesCS4B01G394700 chr6A 3635537 3636236 699 False 1254.000000 1254 99.000000 1 700 1 chr6A.!!$F1 699
17 TraesCS4B01G394700 chr6A 213835162 213835987 825 True 1146.000000 1146 91.787000 2255 3077 1 chr6A.!!$R2 822
18 TraesCS4B01G394700 chr6A 45066717 45067311 594 True 621.000000 621 85.809000 2471 3063 1 chr6A.!!$R1 592
19 TraesCS4B01G394700 chr4A 741027559 741028257 698 False 1253.000000 1253 99.000000 1 700 1 chr4A.!!$F1 699
20 TraesCS4B01G394700 chr4A 604104176 604105189 1013 True 538.000000 538 77.083000 1013 2032 1 chr4A.!!$R2 1019
21 TraesCS4B01G394700 chr4A 663695198 663696135 937 True 501.000000 501 77.213000 1009 1956 1 chr4A.!!$R3 947
22 TraesCS4B01G394700 chr2A 750961166 750961865 699 False 1249.000000 1249 98.857000 1 700 1 chr2A.!!$F3 699
23 TraesCS4B01G394700 chr2A 15959827 15960726 899 False 496.000000 496 77.534000 1030 1956 1 chr2A.!!$F2 926
24 TraesCS4B01G394700 chr2A 15756477 15757383 906 False 431.000000 431 76.105000 1030 1951 1 chr2A.!!$F1 921
25 TraesCS4B01G394700 chr7A 637994380 637995441 1061 False 1020.000000 1020 84.051000 1001 2086 1 chr7A.!!$F1 1085
26 TraesCS4B01G394700 chr7A 638132174 638133210 1036 False 815.000000 815 81.118000 1001 2081 1 chr7A.!!$F2 1080
27 TraesCS4B01G394700 chr7A 51661570 51662508 938 True 479.000000 479 76.829000 1009 1956 1 chr7A.!!$R1 947
28 TraesCS4B01G394700 chr7D 552325048 552326109 1061 False 1003.000000 1003 83.776000 1001 2086 1 chr7D.!!$F1 1085
29 TraesCS4B01G394700 chr1A 440683192 440683986 794 False 981.000000 981 88.875000 2256 3068 1 chr1A.!!$F2 812
30 TraesCS4B01G394700 chr1A 71784572 71785426 854 False 350.000000 350 74.724000 1002 1899 1 chr1A.!!$F1 897
31 TraesCS4B01G394700 chr5D 558955982 558956952 970 True 693.000000 693 79.861000 1034 2031 1 chr5D.!!$R1 997
32 TraesCS4B01G394700 chr5D 560224906 560225824 918 False 492.000000 492 77.259000 1010 1966 1 chr5D.!!$F1 956
33 TraesCS4B01G394700 chr1B 108839264 108839867 603 False 675.000000 675 87.134000 2476 3075 1 chr1B.!!$F1 599
34 TraesCS4B01G394700 chr2B 73270053 73270666 613 True 640.000000 640 86.058000 2476 3075 1 chr2B.!!$R1 599
35 TraesCS4B01G394700 chr1D 72497923 72498643 720 False 353.000000 353 76.084000 1006 1759 1 chr1D.!!$F1 753

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
708 710 0.173255 AAAATCATTTCGCAGGCCGG 59.827 50.0 0.0 0.0 37.59 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2214 2338 0.034476 GTTTTTCGGACGGAGGGAGT 59.966 55.0 0.0 0.0 0.0 3.85 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
83 84 2.517959 TCTCCAAACCAGAAATGGCAG 58.482 47.619 0.00 0.00 34.13 4.85
707 709 1.548986 GAAAATCATTTCGCAGGCCG 58.451 50.000 0.00 0.00 35.94 6.13
708 710 0.173255 AAAATCATTTCGCAGGCCGG 59.827 50.000 0.00 0.00 37.59 6.13
709 711 2.283472 AAATCATTTCGCAGGCCGGC 62.283 55.000 21.18 21.18 37.59 6.13
718 720 4.923942 CAGGCCGGCGCAGATCAT 62.924 66.667 22.54 0.00 36.38 2.45
719 721 4.615815 AGGCCGGCGCAGATCATC 62.616 66.667 22.54 2.36 36.38 2.92
725 727 2.590007 GCGCAGATCATCGCCCTT 60.590 61.111 17.34 0.00 45.01 3.95
726 728 2.182842 GCGCAGATCATCGCCCTTT 61.183 57.895 17.34 0.00 45.01 3.11
727 729 1.937391 CGCAGATCATCGCCCTTTC 59.063 57.895 0.00 0.00 0.00 2.62
728 730 0.811219 CGCAGATCATCGCCCTTTCA 60.811 55.000 0.00 0.00 0.00 2.69
729 731 0.942962 GCAGATCATCGCCCTTTCAG 59.057 55.000 0.00 0.00 0.00 3.02
730 732 1.473965 GCAGATCATCGCCCTTTCAGA 60.474 52.381 0.00 0.00 0.00 3.27
731 733 2.910199 CAGATCATCGCCCTTTCAGAA 58.090 47.619 0.00 0.00 0.00 3.02
732 734 2.871022 CAGATCATCGCCCTTTCAGAAG 59.129 50.000 0.00 0.00 0.00 2.85
751 753 3.543680 AGGTATCCAAAGACGATGGTG 57.456 47.619 0.00 0.00 39.09 4.17
752 754 2.838202 AGGTATCCAAAGACGATGGTGT 59.162 45.455 0.00 0.00 39.09 4.16
753 755 3.118738 AGGTATCCAAAGACGATGGTGTC 60.119 47.826 0.00 0.00 39.09 3.67
782 784 4.890581 CCATGCTCCTACTCTACTAGTGTT 59.109 45.833 5.39 0.00 39.39 3.32
783 785 5.221145 CCATGCTCCTACTCTACTAGTGTTG 60.221 48.000 5.39 0.00 39.39 3.33
784 786 4.919793 TGCTCCTACTCTACTAGTGTTGT 58.080 43.478 5.39 3.82 39.39 3.32
785 787 5.322754 TGCTCCTACTCTACTAGTGTTGTT 58.677 41.667 5.39 0.00 39.39 2.83
786 788 6.479006 TGCTCCTACTCTACTAGTGTTGTTA 58.521 40.000 5.39 0.00 39.39 2.41
787 789 7.117397 TGCTCCTACTCTACTAGTGTTGTTAT 58.883 38.462 5.39 0.00 39.39 1.89
814 816 6.182627 TCCTACTAGGTAAAAGTCATGTCGA 58.817 40.000 1.83 0.00 36.53 4.20
815 817 6.832384 TCCTACTAGGTAAAAGTCATGTCGAT 59.168 38.462 1.83 0.00 36.53 3.59
816 818 6.918569 CCTACTAGGTAAAAGTCATGTCGATG 59.081 42.308 0.00 0.00 0.00 3.84
817 819 5.661458 ACTAGGTAAAAGTCATGTCGATGG 58.339 41.667 0.00 0.00 0.00 3.51
877 880 2.205074 GCCACCATCGATACAGACAAG 58.795 52.381 0.00 0.00 0.00 3.16
912 915 2.389059 CATGACACCGATCGATCACTC 58.611 52.381 24.40 12.55 0.00 3.51
915 918 0.456221 ACACCGATCGATCACTCACC 59.544 55.000 24.40 0.00 0.00 4.02
920 923 1.338020 CGATCGATCACTCACCCATCA 59.662 52.381 24.40 0.00 0.00 3.07
923 926 0.536724 CGATCACTCACCCATCACCA 59.463 55.000 0.00 0.00 0.00 4.17
928 931 1.136329 ACTCACCCATCACCAGCCTT 61.136 55.000 0.00 0.00 0.00 4.35
929 932 0.911769 CTCACCCATCACCAGCCTTA 59.088 55.000 0.00 0.00 0.00 2.69
930 933 0.618458 TCACCCATCACCAGCCTTAC 59.382 55.000 0.00 0.00 0.00 2.34
931 934 0.620556 CACCCATCACCAGCCTTACT 59.379 55.000 0.00 0.00 0.00 2.24
932 935 0.912486 ACCCATCACCAGCCTTACTC 59.088 55.000 0.00 0.00 0.00 2.59
933 936 0.181350 CCCATCACCAGCCTTACTCC 59.819 60.000 0.00 0.00 0.00 3.85
934 937 1.207791 CCATCACCAGCCTTACTCCT 58.792 55.000 0.00 0.00 0.00 3.69
935 938 2.398588 CCATCACCAGCCTTACTCCTA 58.601 52.381 0.00 0.00 0.00 2.94
936 939 2.975489 CCATCACCAGCCTTACTCCTAT 59.025 50.000 0.00 0.00 0.00 2.57
937 940 4.160329 CCATCACCAGCCTTACTCCTATA 58.840 47.826 0.00 0.00 0.00 1.31
938 941 4.021016 CCATCACCAGCCTTACTCCTATAC 60.021 50.000 0.00 0.00 0.00 1.47
939 942 4.259933 TCACCAGCCTTACTCCTATACA 57.740 45.455 0.00 0.00 0.00 2.29
948 951 6.095160 AGCCTTACTCCTATACATACATACGC 59.905 42.308 0.00 0.00 0.00 4.42
953 956 5.106791 ACTCCTATACATACATACGCGTGTC 60.107 44.000 24.59 0.00 33.62 3.67
954 957 4.756135 TCCTATACATACATACGCGTGTCA 59.244 41.667 24.59 1.10 33.62 3.58
956 959 1.556564 ACATACATACGCGTGTCAGC 58.443 50.000 24.59 0.00 33.62 4.26
957 960 1.135228 ACATACATACGCGTGTCAGCA 60.135 47.619 24.59 0.00 36.85 4.41
997 1010 2.355445 TAGCTGCCTTCATCGAGCGG 62.355 60.000 0.00 0.00 36.52 5.52
1764 1845 3.450115 CTCGTGGACGACCCCCTC 61.450 72.222 0.34 0.00 44.22 4.30
1769 1850 4.437587 GGACGACCCCCTCGAGGA 62.438 72.222 33.39 0.00 46.14 3.71
1770 1851 3.139469 GACGACCCCCTCGAGGAC 61.139 72.222 33.39 18.23 46.14 3.85
2110 2234 3.365969 GCATCCGTCCGTTCAAAAGAAAT 60.366 43.478 0.00 0.00 0.00 2.17
2112 2236 5.618195 GCATCCGTCCGTTCAAAAGAAATAA 60.618 40.000 0.00 0.00 0.00 1.40
2113 2237 5.347012 TCCGTCCGTTCAAAAGAAATAAC 57.653 39.130 0.00 0.00 0.00 1.89
2152 2276 7.942341 TCCTATTGAGGCAAAACCGAATATATT 59.058 33.333 0.00 0.00 46.52 1.28
2190 2314 6.091034 GTGATTCATCGGATCTCAGATCATTG 59.909 42.308 16.76 10.06 0.00 2.82
2193 2317 6.847421 TCATCGGATCTCAGATCATTGTAT 57.153 37.500 16.76 0.00 0.00 2.29
2194 2318 7.944729 TCATCGGATCTCAGATCATTGTATA 57.055 36.000 16.76 0.00 0.00 1.47
2195 2319 8.530804 TCATCGGATCTCAGATCATTGTATAT 57.469 34.615 16.76 0.00 0.00 0.86
2196 2320 9.632638 TCATCGGATCTCAGATCATTGTATATA 57.367 33.333 16.76 0.00 0.00 0.86
2212 2336 9.894783 CATTGTATATATATGCGAGTACCTACC 57.105 37.037 5.44 0.00 0.00 3.18
2213 2337 9.863650 ATTGTATATATATGCGAGTACCTACCT 57.136 33.333 5.44 0.00 0.00 3.08
2215 2339 9.770097 TGTATATATATGCGAGTACCTACCTAC 57.230 37.037 5.44 0.00 0.00 3.18
2216 2340 9.995003 GTATATATATGCGAGTACCTACCTACT 57.005 37.037 5.44 0.00 0.00 2.57
2218 2342 2.338577 TGCGAGTACCTACCTACTCC 57.661 55.000 0.00 0.00 39.66 3.85
2219 2343 1.133976 TGCGAGTACCTACCTACTCCC 60.134 57.143 0.00 0.00 39.66 4.30
2220 2344 1.142667 GCGAGTACCTACCTACTCCCT 59.857 57.143 0.00 0.00 39.66 4.20
2221 2345 2.810032 GCGAGTACCTACCTACTCCCTC 60.810 59.091 0.00 0.00 39.66 4.30
2222 2346 2.224499 CGAGTACCTACCTACTCCCTCC 60.224 59.091 0.00 0.00 39.66 4.30
2223 2347 1.773653 AGTACCTACCTACTCCCTCCG 59.226 57.143 0.00 0.00 0.00 4.63
2224 2348 1.492599 GTACCTACCTACTCCCTCCGT 59.507 57.143 0.00 0.00 0.00 4.69
2225 2349 0.550432 ACCTACCTACTCCCTCCGTC 59.450 60.000 0.00 0.00 0.00 4.79
2226 2350 0.178995 CCTACCTACTCCCTCCGTCC 60.179 65.000 0.00 0.00 0.00 4.79
2227 2351 0.534652 CTACCTACTCCCTCCGTCCG 60.535 65.000 0.00 0.00 0.00 4.79
2228 2352 0.982852 TACCTACTCCCTCCGTCCGA 60.983 60.000 0.00 0.00 0.00 4.55
2229 2353 1.077212 CCTACTCCCTCCGTCCGAA 60.077 63.158 0.00 0.00 0.00 4.30
2230 2354 0.682209 CCTACTCCCTCCGTCCGAAA 60.682 60.000 0.00 0.00 0.00 3.46
2231 2355 1.180029 CTACTCCCTCCGTCCGAAAA 58.820 55.000 0.00 0.00 0.00 2.29
2232 2356 1.547372 CTACTCCCTCCGTCCGAAAAA 59.453 52.381 0.00 0.00 0.00 1.94
2233 2357 0.034476 ACTCCCTCCGTCCGAAAAAC 59.966 55.000 0.00 0.00 0.00 2.43
2234 2358 0.672711 CTCCCTCCGTCCGAAAAACC 60.673 60.000 0.00 0.00 0.00 3.27
2235 2359 1.123246 TCCCTCCGTCCGAAAAACCT 61.123 55.000 0.00 0.00 0.00 3.50
2236 2360 0.250597 CCCTCCGTCCGAAAAACCTT 60.251 55.000 0.00 0.00 0.00 3.50
2237 2361 0.872388 CCTCCGTCCGAAAAACCTTG 59.128 55.000 0.00 0.00 0.00 3.61
2238 2362 1.589803 CTCCGTCCGAAAAACCTTGT 58.410 50.000 0.00 0.00 0.00 3.16
2239 2363 1.529865 CTCCGTCCGAAAAACCTTGTC 59.470 52.381 0.00 0.00 0.00 3.18
2240 2364 0.589708 CCGTCCGAAAAACCTTGTCC 59.410 55.000 0.00 0.00 0.00 4.02
2241 2365 1.301423 CGTCCGAAAAACCTTGTCCA 58.699 50.000 0.00 0.00 0.00 4.02
2242 2366 1.671845 CGTCCGAAAAACCTTGTCCAA 59.328 47.619 0.00 0.00 0.00 3.53
2243 2367 2.097791 CGTCCGAAAAACCTTGTCCAAA 59.902 45.455 0.00 0.00 0.00 3.28
2244 2368 3.702330 GTCCGAAAAACCTTGTCCAAAG 58.298 45.455 0.00 0.00 0.00 2.77
2245 2369 2.100087 TCCGAAAAACCTTGTCCAAAGC 59.900 45.455 0.00 0.00 0.00 3.51
2246 2370 2.100749 CCGAAAAACCTTGTCCAAAGCT 59.899 45.455 0.00 0.00 0.00 3.74
2247 2371 3.316868 CCGAAAAACCTTGTCCAAAGCTA 59.683 43.478 0.00 0.00 0.00 3.32
2248 2372 4.022329 CCGAAAAACCTTGTCCAAAGCTAT 60.022 41.667 0.00 0.00 0.00 2.97
2249 2373 5.508994 CCGAAAAACCTTGTCCAAAGCTATT 60.509 40.000 0.00 0.00 0.00 1.73
2250 2374 5.629435 CGAAAAACCTTGTCCAAAGCTATTC 59.371 40.000 0.00 0.00 0.00 1.75
2251 2375 5.468540 AAAACCTTGTCCAAAGCTATTCC 57.531 39.130 0.00 0.00 0.00 3.01
2252 2376 4.388577 AACCTTGTCCAAAGCTATTCCT 57.611 40.909 0.00 0.00 0.00 3.36
2253 2377 3.956744 ACCTTGTCCAAAGCTATTCCTC 58.043 45.455 0.00 0.00 0.00 3.71
2335 2459 2.547007 CGCCCGATACATACATCCACAA 60.547 50.000 0.00 0.00 0.00 3.33
2461 2585 2.286523 CCCTCCGACTTGGCTCACT 61.287 63.158 0.00 0.00 37.80 3.41
2595 2737 2.262572 GCGGTAGCACAAATCAAAGG 57.737 50.000 0.00 0.00 44.35 3.11
2636 2778 6.585322 ACAAAACGACGGTAACAAAATTTTGA 59.415 30.769 32.20 12.38 40.55 2.69
2697 2840 8.421002 ACATCAAAAACAAGGTAGTAGCAAAAT 58.579 29.630 1.58 0.00 0.00 1.82
2818 2969 6.590234 AAAGGATGGTAGCAAAAACTAAGG 57.410 37.500 0.00 0.00 0.00 2.69
3068 3233 3.687321 ATGCCATCGACTGCGGCTT 62.687 57.895 15.51 8.48 46.39 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
83 84 4.036144 GCTTCTTGATATCCTTTGCTCACC 59.964 45.833 0.00 0.00 0.00 4.02
462 463 9.255304 CAGGAGAGATCTTATAAACTTTAGCAC 57.745 37.037 0.00 0.00 0.00 4.40
709 711 0.811219 TGAAAGGGCGATGATCTGCG 60.811 55.000 0.00 0.00 0.00 5.18
710 712 0.942962 CTGAAAGGGCGATGATCTGC 59.057 55.000 0.00 1.58 0.00 4.26
711 713 2.609427 TCTGAAAGGGCGATGATCTG 57.391 50.000 0.00 0.00 0.00 2.90
712 714 3.191078 CTTCTGAAAGGGCGATGATCT 57.809 47.619 0.00 0.00 0.00 2.75
723 725 5.479306 TCGTCTTTGGATACCTTCTGAAAG 58.521 41.667 0.00 0.00 0.00 2.62
724 726 5.477607 TCGTCTTTGGATACCTTCTGAAA 57.522 39.130 0.00 0.00 0.00 2.69
725 727 5.419542 CATCGTCTTTGGATACCTTCTGAA 58.580 41.667 0.00 0.00 0.00 3.02
726 728 4.141937 CCATCGTCTTTGGATACCTTCTGA 60.142 45.833 0.00 0.00 36.26 3.27
727 729 4.122776 CCATCGTCTTTGGATACCTTCTG 58.877 47.826 0.00 0.00 36.26 3.02
728 730 3.775316 ACCATCGTCTTTGGATACCTTCT 59.225 43.478 0.00 0.00 37.69 2.85
729 731 3.871594 CACCATCGTCTTTGGATACCTTC 59.128 47.826 0.00 0.00 37.69 3.46
730 732 3.263425 ACACCATCGTCTTTGGATACCTT 59.737 43.478 0.00 0.00 37.69 3.50
731 733 2.838202 ACACCATCGTCTTTGGATACCT 59.162 45.455 0.00 0.00 37.69 3.08
732 734 3.195661 GACACCATCGTCTTTGGATACC 58.804 50.000 0.00 0.00 37.69 2.73
733 735 2.858344 CGACACCATCGTCTTTGGATAC 59.142 50.000 0.00 0.00 46.25 2.24
734 736 3.159353 CGACACCATCGTCTTTGGATA 57.841 47.619 0.00 0.00 46.25 2.59
735 737 2.010145 CGACACCATCGTCTTTGGAT 57.990 50.000 0.00 0.00 46.25 3.41
736 738 3.507597 CGACACCATCGTCTTTGGA 57.492 52.632 0.00 0.00 46.25 3.53
751 753 1.683917 AGTAGGAGCATGGATGTCGAC 59.316 52.381 9.11 9.11 0.00 4.20
752 754 1.957177 GAGTAGGAGCATGGATGTCGA 59.043 52.381 0.00 0.00 0.00 4.20
753 755 1.959985 AGAGTAGGAGCATGGATGTCG 59.040 52.381 0.00 0.00 0.00 4.35
782 784 9.979897 TGACTTTTACCTAGTAGGAGTATAACA 57.020 33.333 23.50 11.57 37.67 2.41
786 788 9.134055 GACATGACTTTTACCTAGTAGGAGTAT 57.866 37.037 23.50 2.61 37.67 2.12
787 789 7.281774 CGACATGACTTTTACCTAGTAGGAGTA 59.718 40.741 23.50 2.71 37.67 2.59
807 809 3.576356 GCGTGCCCCATCGACATG 61.576 66.667 0.00 0.00 0.00 3.21
814 816 1.530419 TCTTGTTTGCGTGCCCCAT 60.530 52.632 0.00 0.00 0.00 4.00
815 817 2.124109 TCTTGTTTGCGTGCCCCA 60.124 55.556 0.00 0.00 0.00 4.96
816 818 2.010582 TTGTCTTGTTTGCGTGCCCC 62.011 55.000 0.00 0.00 0.00 5.80
817 819 0.031994 ATTGTCTTGTTTGCGTGCCC 59.968 50.000 0.00 0.00 0.00 5.36
827 829 1.608109 TGCGTGCATCAATTGTCTTGT 59.392 42.857 5.13 0.00 0.00 3.16
828 830 2.334971 TGCGTGCATCAATTGTCTTG 57.665 45.000 5.13 3.67 0.00 3.02
829 831 2.871133 CATGCGTGCATCAATTGTCTT 58.129 42.857 3.96 0.00 33.90 3.01
830 832 2.554806 CATGCGTGCATCAATTGTCT 57.445 45.000 3.96 0.00 33.90 3.41
857 859 2.159099 TCTTGTCTGTATCGATGGTGGC 60.159 50.000 8.54 0.00 0.00 5.01
858 860 3.119137 TGTCTTGTCTGTATCGATGGTGG 60.119 47.826 8.54 0.00 0.00 4.61
892 895 2.223572 TGAGTGATCGATCGGTGTCATG 60.224 50.000 20.03 0.00 0.00 3.07
912 915 0.620556 AGTAAGGCTGGTGATGGGTG 59.379 55.000 0.00 0.00 0.00 4.61
915 918 1.207791 AGGAGTAAGGCTGGTGATGG 58.792 55.000 0.00 0.00 0.00 3.51
920 923 5.712752 TGTATGTATAGGAGTAAGGCTGGT 58.287 41.667 0.00 0.00 0.00 4.00
923 926 6.095160 GCGTATGTATGTATAGGAGTAAGGCT 59.905 42.308 0.00 0.00 0.00 4.58
928 931 5.934043 ACACGCGTATGTATGTATAGGAGTA 59.066 40.000 13.44 0.00 32.38 2.59
929 932 4.758674 ACACGCGTATGTATGTATAGGAGT 59.241 41.667 13.44 0.00 33.69 3.85
930 933 5.106830 TGACACGCGTATGTATGTATAGGAG 60.107 44.000 13.44 0.00 31.24 3.69
931 934 4.756135 TGACACGCGTATGTATGTATAGGA 59.244 41.667 13.44 0.00 31.24 2.94
932 935 5.038247 TGACACGCGTATGTATGTATAGG 57.962 43.478 13.44 0.00 31.24 2.57
933 936 4.553815 GCTGACACGCGTATGTATGTATAG 59.446 45.833 13.44 7.92 31.24 1.31
934 937 4.023878 TGCTGACACGCGTATGTATGTATA 60.024 41.667 13.44 0.00 31.24 1.47
935 938 3.243267 TGCTGACACGCGTATGTATGTAT 60.243 43.478 13.44 0.00 31.24 2.29
936 939 2.097791 TGCTGACACGCGTATGTATGTA 59.902 45.455 13.44 0.00 31.24 2.29
937 940 1.135228 TGCTGACACGCGTATGTATGT 60.135 47.619 13.44 3.96 31.24 2.29
938 941 1.255342 GTGCTGACACGCGTATGTATG 59.745 52.381 13.44 0.00 36.98 2.39
939 942 1.556564 GTGCTGACACGCGTATGTAT 58.443 50.000 13.44 0.00 36.98 2.29
960 963 1.315981 TAGCCAGCTCTCACAGTCGG 61.316 60.000 0.00 0.00 0.00 4.79
984 993 1.645455 CATTGCCGCTCGATGAAGG 59.355 57.895 0.00 0.00 38.60 3.46
2086 2210 2.028839 TCTTTTGAACGGACGGATGCTA 60.029 45.455 0.00 0.00 0.00 3.49
2087 2211 1.156736 CTTTTGAACGGACGGATGCT 58.843 50.000 0.00 0.00 0.00 3.79
2088 2212 1.153353 TCTTTTGAACGGACGGATGC 58.847 50.000 0.00 0.00 0.00 3.91
2089 2213 3.889196 TTTCTTTTGAACGGACGGATG 57.111 42.857 0.00 0.00 38.30 3.51
2132 2256 7.554835 ACTGTAAATATATTCGGTTTTGCCTCA 59.445 33.333 0.00 0.00 34.25 3.86
2152 2276 5.872617 CCGATGAATCACACCTAAACTGTAA 59.127 40.000 0.00 0.00 0.00 2.41
2190 2314 9.995003 AGTAGGTAGGTACTCGCATATATATAC 57.005 37.037 0.00 0.00 41.75 1.47
2193 2317 7.504403 GGAGTAGGTAGGTACTCGCATATATA 58.496 42.308 5.24 0.00 46.88 0.86
2194 2318 6.355747 GGAGTAGGTAGGTACTCGCATATAT 58.644 44.000 5.24 0.00 46.88 0.86
2195 2319 5.738909 GGAGTAGGTAGGTACTCGCATATA 58.261 45.833 5.24 0.00 46.88 0.86
2196 2320 4.587891 GGAGTAGGTAGGTACTCGCATAT 58.412 47.826 5.24 0.00 46.88 1.78
2197 2321 4.013267 GGAGTAGGTAGGTACTCGCATA 57.987 50.000 5.24 0.00 46.88 3.14
2198 2322 2.861274 GGAGTAGGTAGGTACTCGCAT 58.139 52.381 5.24 0.00 46.88 4.73
2199 2323 2.338577 GGAGTAGGTAGGTACTCGCA 57.661 55.000 5.24 0.00 46.88 5.10
2201 2325 2.224499 GGAGGGAGTAGGTAGGTACTCG 60.224 59.091 5.24 0.00 46.88 4.18
2202 2326 2.224499 CGGAGGGAGTAGGTAGGTACTC 60.224 59.091 2.93 2.93 45.70 2.59
2203 2327 1.773653 CGGAGGGAGTAGGTAGGTACT 59.226 57.143 0.00 0.00 46.37 2.73
2204 2328 1.492599 ACGGAGGGAGTAGGTAGGTAC 59.507 57.143 0.00 0.00 0.00 3.34
2205 2329 1.771255 GACGGAGGGAGTAGGTAGGTA 59.229 57.143 0.00 0.00 0.00 3.08
2206 2330 0.550432 GACGGAGGGAGTAGGTAGGT 59.450 60.000 0.00 0.00 0.00 3.08
2207 2331 0.178995 GGACGGAGGGAGTAGGTAGG 60.179 65.000 0.00 0.00 0.00 3.18
2208 2332 0.534652 CGGACGGAGGGAGTAGGTAG 60.535 65.000 0.00 0.00 0.00 3.18
2209 2333 0.982852 TCGGACGGAGGGAGTAGGTA 60.983 60.000 0.00 0.00 0.00 3.08
2210 2334 1.856539 TTCGGACGGAGGGAGTAGGT 61.857 60.000 0.00 0.00 0.00 3.08
2211 2335 0.682209 TTTCGGACGGAGGGAGTAGG 60.682 60.000 0.00 0.00 0.00 3.18
2212 2336 1.180029 TTTTCGGACGGAGGGAGTAG 58.820 55.000 0.00 0.00 0.00 2.57
2213 2337 1.273327 GTTTTTCGGACGGAGGGAGTA 59.727 52.381 0.00 0.00 0.00 2.59
2214 2338 0.034476 GTTTTTCGGACGGAGGGAGT 59.966 55.000 0.00 0.00 0.00 3.85
2215 2339 0.672711 GGTTTTTCGGACGGAGGGAG 60.673 60.000 0.00 0.00 0.00 4.30
2216 2340 1.123246 AGGTTTTTCGGACGGAGGGA 61.123 55.000 0.00 0.00 0.00 4.20
2217 2341 0.250597 AAGGTTTTTCGGACGGAGGG 60.251 55.000 0.00 0.00 0.00 4.30
2218 2342 0.872388 CAAGGTTTTTCGGACGGAGG 59.128 55.000 0.00 0.00 0.00 4.30
2219 2343 1.529865 GACAAGGTTTTTCGGACGGAG 59.470 52.381 0.00 0.00 0.00 4.63
2220 2344 1.585297 GACAAGGTTTTTCGGACGGA 58.415 50.000 0.00 0.00 0.00 4.69
2221 2345 0.589708 GGACAAGGTTTTTCGGACGG 59.410 55.000 0.00 0.00 0.00 4.79
2222 2346 1.301423 TGGACAAGGTTTTTCGGACG 58.699 50.000 0.00 0.00 0.00 4.79
2223 2347 3.702330 CTTTGGACAAGGTTTTTCGGAC 58.298 45.455 0.00 0.00 0.00 4.79
2224 2348 2.100087 GCTTTGGACAAGGTTTTTCGGA 59.900 45.455 0.00 0.00 0.00 4.55
2225 2349 2.100749 AGCTTTGGACAAGGTTTTTCGG 59.899 45.455 0.00 0.00 0.00 4.30
2226 2350 3.436700 AGCTTTGGACAAGGTTTTTCG 57.563 42.857 0.00 0.00 0.00 3.46
2227 2351 5.926542 GGAATAGCTTTGGACAAGGTTTTTC 59.073 40.000 0.00 5.96 0.00 2.29
2228 2352 5.602561 AGGAATAGCTTTGGACAAGGTTTTT 59.397 36.000 0.00 0.00 0.00 1.94
2229 2353 5.147767 AGGAATAGCTTTGGACAAGGTTTT 58.852 37.500 0.00 0.00 0.00 2.43
2230 2354 4.740902 AGGAATAGCTTTGGACAAGGTTT 58.259 39.130 0.00 0.00 0.00 3.27
2231 2355 4.202567 TGAGGAATAGCTTTGGACAAGGTT 60.203 41.667 0.00 0.00 0.00 3.50
2232 2356 3.330701 TGAGGAATAGCTTTGGACAAGGT 59.669 43.478 0.00 0.00 0.00 3.50
2233 2357 3.955471 TGAGGAATAGCTTTGGACAAGG 58.045 45.455 0.00 0.00 0.00 3.61
2234 2358 5.105997 CCTTTGAGGAATAGCTTTGGACAAG 60.106 44.000 0.00 0.00 37.67 3.16
2235 2359 4.766891 CCTTTGAGGAATAGCTTTGGACAA 59.233 41.667 0.00 0.00 37.67 3.18
2236 2360 4.335416 CCTTTGAGGAATAGCTTTGGACA 58.665 43.478 0.00 0.00 37.67 4.02
2237 2361 3.129462 GCCTTTGAGGAATAGCTTTGGAC 59.871 47.826 0.00 0.00 37.67 4.02
2238 2362 3.356290 GCCTTTGAGGAATAGCTTTGGA 58.644 45.455 0.00 0.00 37.67 3.53
2239 2363 2.428530 GGCCTTTGAGGAATAGCTTTGG 59.571 50.000 0.00 0.00 37.67 3.28
2240 2364 3.091545 TGGCCTTTGAGGAATAGCTTTG 58.908 45.455 3.32 0.00 37.67 2.77
2241 2365 3.092301 GTGGCCTTTGAGGAATAGCTTT 58.908 45.455 3.32 0.00 37.67 3.51
2242 2366 2.621668 GGTGGCCTTTGAGGAATAGCTT 60.622 50.000 3.32 0.00 37.67 3.74
2243 2367 1.064389 GGTGGCCTTTGAGGAATAGCT 60.064 52.381 3.32 0.00 37.67 3.32
2244 2368 1.340991 TGGTGGCCTTTGAGGAATAGC 60.341 52.381 3.32 0.00 37.67 2.97
2245 2369 2.025887 AGTGGTGGCCTTTGAGGAATAG 60.026 50.000 3.32 0.00 37.67 1.73
2246 2370 1.992557 AGTGGTGGCCTTTGAGGAATA 59.007 47.619 3.32 0.00 37.67 1.75
2247 2371 0.779997 AGTGGTGGCCTTTGAGGAAT 59.220 50.000 3.32 0.00 37.67 3.01
2248 2372 1.351017 CTAGTGGTGGCCTTTGAGGAA 59.649 52.381 3.32 0.00 37.67 3.36
2249 2373 0.984230 CTAGTGGTGGCCTTTGAGGA 59.016 55.000 3.32 0.00 37.67 3.71
2250 2374 0.035056 CCTAGTGGTGGCCTTTGAGG 60.035 60.000 3.32 0.00 38.80 3.86
2251 2375 0.678048 GCCTAGTGGTGGCCTTTGAG 60.678 60.000 3.32 0.00 44.32 3.02
2252 2376 1.378762 GCCTAGTGGTGGCCTTTGA 59.621 57.895 3.32 0.00 44.32 2.69
2253 2377 4.002797 GCCTAGTGGTGGCCTTTG 57.997 61.111 3.32 0.00 44.32 2.77
2335 2459 2.822399 GGGATCCAATCGAGCGGT 59.178 61.111 15.23 0.00 0.00 5.68
2432 2556 0.618981 GTCGGAGGGGGACTTCAATT 59.381 55.000 0.00 0.00 38.40 2.32
2577 2719 1.539388 TGCCTTTGATTTGTGCTACCG 59.461 47.619 0.00 0.00 0.00 4.02
2620 2762 7.436673 TGGAATCACTTCAAAATTTTGTTACCG 59.563 33.333 25.98 14.34 39.18 4.02
2636 2778 4.834496 TCCATCTTTTTGCTGGAATCACTT 59.166 37.500 0.00 0.00 37.95 3.16
2697 2840 2.165167 ACCACCGTCTTCGTCTTCATA 58.835 47.619 0.00 0.00 35.01 2.15
2818 2969 2.734276 TTTATTTTTGCCACCTCCGC 57.266 45.000 0.00 0.00 0.00 5.54
3014 3179 6.303839 TCTGGTTACTACTTTTGCTGGAATT 58.696 36.000 0.00 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.