Multiple sequence alignment - TraesCS7B01G014300

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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 TraesCS7B01G014300 chr7B 100.000 5840 0 0 1 5840 10891032 10896871 0.000000e+00 10785.0
1 TraesCS7B01G014300 chr7B 95.978 2163 56 11 2560 4721 10881357 10883489 0.000000e+00 3483.0
2 TraesCS7B01G014300 chr7B 93.727 813 42 4 4923 5731 10883618 10884425 0.000000e+00 1210.0
3 TraesCS7B01G014300 chr7B 88.814 885 76 16 1364 2235 694352827 694353701 0.000000e+00 1064.0
4 TraesCS7B01G014300 chr7B 94.951 614 14 9 769 1365 10880750 10881363 0.000000e+00 946.0
5 TraesCS7B01G014300 chr7B 90.588 340 23 5 2221 2555 694353763 694354098 5.370000e-120 442.0
6 TraesCS7B01G014300 chr7B 98.519 135 2 0 863 997 10819944 10820078 7.560000e-59 239.0
7 TraesCS7B01G014300 chr7B 96.947 131 4 0 4780 4910 10883506 10883636 2.740000e-53 220.0
8 TraesCS7B01G014300 chrUn 95.978 2163 56 11 2560 4721 305654727 305656859 0.000000e+00 3483.0
9 TraesCS7B01G014300 chrUn 95.978 2163 56 11 2560 4721 308151592 308149460 0.000000e+00 3483.0
10 TraesCS7B01G014300 chrUn 95.978 2163 56 11 2560 4721 308155700 308153568 0.000000e+00 3483.0
11 TraesCS7B01G014300 chrUn 98.108 1374 17 5 1 1365 305653360 305654733 0.000000e+00 2385.0
12 TraesCS7B01G014300 chrUn 93.727 813 42 4 4923 5731 308153439 308152632 0.000000e+00 1210.0
13 TraesCS7B01G014300 chrUn 93.604 813 43 4 4923 5731 308149331 308148524 0.000000e+00 1205.0
14 TraesCS7B01G014300 chrUn 96.133 543 21 0 3573 4115 32229729 32229187 0.000000e+00 887.0
15 TraesCS7B01G014300 chrUn 86.803 538 52 11 1710 2235 319198478 319199008 3.030000e-162 582.0
16 TraesCS7B01G014300 chrUn 86.803 538 52 11 1710 2235 347747279 347747809 3.030000e-162 582.0
17 TraesCS7B01G014300 chrUn 91.404 349 25 3 1366 1712 319198052 319198397 1.900000e-129 473.0
18 TraesCS7B01G014300 chrUn 91.318 311 23 4 2248 2555 319199140 319199449 7.000000e-114 422.0
19 TraesCS7B01G014300 chrUn 91.318 311 23 4 2248 2555 347747941 347748250 7.000000e-114 422.0
20 TraesCS7B01G014300 chrUn 97.710 131 3 0 4780 4910 308149443 308149313 5.890000e-55 226.0
21 TraesCS7B01G014300 chrUn 96.947 131 4 0 4780 4910 308153551 308153421 2.740000e-53 220.0
22 TraesCS7B01G014300 chrUn 97.581 124 3 0 4780 4903 305656876 305656999 4.580000e-51 213.0
23 TraesCS7B01G014300 chrUn 95.122 82 3 1 537 618 84535335 84535415 1.710000e-25 128.0
24 TraesCS7B01G014300 chrUn 91.667 60 4 1 640 699 328116236 328116294 1.350000e-11 82.4
25 TraesCS7B01G014300 chr4B 95.409 1198 39 3 1365 2554 554987501 554988690 0.000000e+00 1893.0
26 TraesCS7B01G014300 chr6A 94.583 1200 45 5 1365 2554 57422580 57421391 0.000000e+00 1838.0
27 TraesCS7B01G014300 chr6A 96.317 543 20 0 3573 4115 527455237 527455779 0.000000e+00 893.0
28 TraesCS7B01G014300 chr6B 94.516 1094 47 6 2813 3905 360922870 360921789 0.000000e+00 1676.0
29 TraesCS7B01G014300 chr3D 95.848 867 28 2 1364 2229 34045231 34046090 0.000000e+00 1395.0
30 TraesCS7B01G014300 chr3D 92.655 531 35 4 5 534 262776006 262775479 0.000000e+00 761.0
31 TraesCS7B01G014300 chr3D 92.135 534 35 6 2 534 47284593 47285120 0.000000e+00 747.0
32 TraesCS7B01G014300 chr3D 94.985 339 9 3 2221 2558 34046137 34046468 5.180000e-145 525.0
33 TraesCS7B01G014300 chr2B 94.851 874 43 2 1363 2235 147619725 147618853 0.000000e+00 1363.0
34 TraesCS7B01G014300 chr2B 94.737 874 44 2 1363 2235 147643264 147642392 0.000000e+00 1358.0
35 TraesCS7B01G014300 chr2B 92.308 338 16 5 2221 2557 147618768 147618440 6.850000e-129 472.0
36 TraesCS7B01G014300 chr2B 92.308 338 16 5 2221 2557 147642351 147642023 6.850000e-129 472.0
37 TraesCS7B01G014300 chr7D 91.880 936 37 15 4923 5840 65937169 65936255 0.000000e+00 1271.0
38 TraesCS7B01G014300 chr7D 89.389 999 46 25 2558 3530 69041963 69042927 0.000000e+00 1203.0
39 TraesCS7B01G014300 chr7D 91.397 895 27 11 3855 4721 65938169 65937297 0.000000e+00 1181.0
40 TraesCS7B01G014300 chr7D 92.308 624 20 14 769 1364 69041347 69041970 0.000000e+00 861.0
41 TraesCS7B01G014300 chr7D 91.080 639 49 2 2880 3518 65939561 65938931 0.000000e+00 857.0
42 TraesCS7B01G014300 chr7D 96.450 507 16 2 4193 4699 69043495 69043999 0.000000e+00 835.0
43 TraesCS7B01G014300 chr7D 87.793 598 20 11 4781 5377 69043998 69044543 0.000000e+00 651.0
44 TraesCS7B01G014300 chr7D 83.622 751 55 26 630 1364 66348660 66347962 1.370000e-180 643.0
45 TraesCS7B01G014300 chr7D 95.856 362 15 0 5370 5731 69048027 69048388 2.340000e-163 586.0
46 TraesCS7B01G014300 chr7D 81.972 649 101 11 2561 3206 66347966 66347331 2.390000e-148 536.0
47 TraesCS7B01G014300 chr7D 89.013 446 27 10 938 1364 65940372 65939930 3.100000e-147 532.0
48 TraesCS7B01G014300 chr7D 87.445 454 45 6 4249 4696 68909473 68909920 4.040000e-141 512.0
49 TraesCS7B01G014300 chr7D 90.728 302 19 1 2558 2850 65939937 65939636 1.530000e-105 394.0
50 TraesCS7B01G014300 chr7D 95.397 239 9 2 536 774 69031119 69031355 4.270000e-101 379.0
51 TraesCS7B01G014300 chr7D 94.891 137 5 2 4780 4915 65937280 65937145 4.580000e-51 213.0
52 TraesCS7B01G014300 chr7D 90.196 153 13 2 5488 5639 65900600 65900449 1.280000e-46 198.0
53 TraesCS7B01G014300 chr7A 94.048 840 32 6 536 1364 74684195 74685027 0.000000e+00 1258.0
54 TraesCS7B01G014300 chr7A 91.506 777 45 12 3573 4349 6035822 6036577 0.000000e+00 1050.0
55 TraesCS7B01G014300 chr7A 94.181 653 31 1 2873 3525 74685249 74685894 0.000000e+00 989.0
56 TraesCS7B01G014300 chr7A 94.625 614 20 4 5240 5840 70733835 70733222 0.000000e+00 939.0
57 TraesCS7B01G014300 chr7A 95.752 565 24 0 1364 1928 5355390 5355954 0.000000e+00 911.0
58 TraesCS7B01G014300 chr7A 95.772 544 21 2 4179 4721 70734782 70734240 0.000000e+00 876.0
59 TraesCS7B01G014300 chr7A 95.069 507 25 0 4193 4699 74686774 74687280 0.000000e+00 798.0
60 TraesCS7B01G014300 chr7A 87.572 692 60 14 683 1364 70767646 70766971 0.000000e+00 778.0
61 TraesCS7B01G014300 chr7A 91.111 495 44 0 2873 3367 70735576 70735082 0.000000e+00 671.0
62 TraesCS7B01G014300 chr7A 90.038 522 41 4 851 1364 70737307 70736789 0.000000e+00 665.0
63 TraesCS7B01G014300 chr7A 94.059 404 21 2 4780 5182 74687296 74687697 1.390000e-170 610.0
64 TraesCS7B01G014300 chr7A 89.154 461 48 2 4236 4696 74594170 74594628 1.830000e-159 573.0
65 TraesCS7B01G014300 chr7A 94.068 354 18 3 5182 5533 74697130 74697482 8.610000e-148 534.0
66 TraesCS7B01G014300 chr7A 85.316 538 45 12 855 1364 70754457 70753926 5.180000e-145 525.0
67 TraesCS7B01G014300 chr7A 81.307 658 90 14 2561 3206 70766975 70766339 2.430000e-138 503.0
68 TraesCS7B01G014300 chr7A 91.824 318 15 2 1929 2235 735984740 735984423 3.230000e-117 433.0
69 TraesCS7B01G014300 chr7A 89.347 291 21 6 4923 5206 70734111 70733824 2.000000e-94 357.0
70 TraesCS7B01G014300 chr7A 83.976 337 47 7 1034 1364 74601175 74601510 3.400000e-82 316.0
71 TraesCS7B01G014300 chr7A 90.805 174 16 0 2558 2731 70736796 70736623 3.520000e-57 233.0
72 TraesCS7B01G014300 chr7A 96.350 137 4 1 4780 4915 70734223 70734087 2.120000e-54 224.0
73 TraesCS7B01G014300 chr7A 91.195 159 2 4 2730 2879 70735763 70735608 7.670000e-49 206.0
74 TraesCS7B01G014300 chr7A 91.045 134 0 4 2755 2879 74685084 74685214 2.800000e-38 171.0
75 TraesCS7B01G014300 chr7A 98.851 87 1 0 5607 5693 74697622 74697708 7.840000e-34 156.0
76 TraesCS7B01G014300 chr7A 93.902 82 4 1 537 618 70769552 70769472 7.950000e-24 122.0
77 TraesCS7B01G014300 chr7A 84.375 96 8 5 632 724 568486146 568486055 2.900000e-13 87.9
78 TraesCS7B01G014300 chr3A 88.128 876 82 14 1363 2223 691451179 691450311 0.000000e+00 1022.0
79 TraesCS7B01G014300 chr1A 90.874 778 44 17 3573 4349 103031065 103030314 0.000000e+00 1018.0
80 TraesCS7B01G014300 chr1A 96.317 543 20 0 3573 4115 8508031 8508573 0.000000e+00 893.0
81 TraesCS7B01G014300 chr4D 93.135 539 31 6 2 538 437895204 437895738 0.000000e+00 785.0
82 TraesCS7B01G014300 chr4D 89.333 75 7 1 630 703 50755435 50755361 6.230000e-15 93.5
83 TraesCS7B01G014300 chr2A 94.242 521 17 4 1364 1884 622807 622300 0.000000e+00 784.0
84 TraesCS7B01G014300 chr2A 92.916 367 15 2 1873 2235 622266 621907 1.860000e-144 523.0
85 TraesCS7B01G014300 chr2A 90.805 348 19 9 2221 2555 621866 621519 2.480000e-123 453.0
86 TraesCS7B01G014300 chr2A 93.333 60 4 0 640 699 18190102 18190043 8.060000e-14 89.8
87 TraesCS7B01G014300 chr1D 92.910 536 33 5 2 534 439692462 439692995 0.000000e+00 774.0
88 TraesCS7B01G014300 chr1D 92.844 531 31 7 5 534 252516113 252515589 0.000000e+00 763.0
89 TraesCS7B01G014300 chr1D 81.905 105 18 1 630 733 30123589 30123485 2.900000e-13 87.9
90 TraesCS7B01G014300 chr2D 92.523 535 34 6 5 538 546255980 546255451 0.000000e+00 761.0
91 TraesCS7B01G014300 chr6D 92.193 538 36 6 5 541 104446911 104446379 0.000000e+00 756.0
92 TraesCS7B01G014300 chr6D 92.135 534 37 5 2 534 205895015 205895544 0.000000e+00 749.0


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 TraesCS7B01G014300 chr7B 10891032 10896871 5839 False 10785.000000 10785 100.000000 1 5840 1 chr7B.!!$F2 5839
1 TraesCS7B01G014300 chr7B 10880750 10884425 3675 False 1464.750000 3483 95.400750 769 5731 4 chr7B.!!$F3 4962
2 TraesCS7B01G014300 chr7B 694352827 694354098 1271 False 753.000000 1064 89.701000 1364 2555 2 chr7B.!!$F4 1191
3 TraesCS7B01G014300 chrUn 305653360 305656999 3639 False 2027.000000 3483 97.222333 1 4903 3 chrUn.!!$F3 4902
4 TraesCS7B01G014300 chrUn 308148524 308155700 7176 True 1637.833333 3483 95.657333 2560 5731 6 chrUn.!!$R2 3171
5 TraesCS7B01G014300 chrUn 32229187 32229729 542 True 887.000000 887 96.133000 3573 4115 1 chrUn.!!$R1 542
6 TraesCS7B01G014300 chrUn 347747279 347748250 971 False 502.000000 582 89.060500 1710 2555 2 chrUn.!!$F5 845
7 TraesCS7B01G014300 chrUn 319198052 319199449 1397 False 492.333333 582 89.841667 1366 2555 3 chrUn.!!$F4 1189
8 TraesCS7B01G014300 chr4B 554987501 554988690 1189 False 1893.000000 1893 95.409000 1365 2554 1 chr4B.!!$F1 1189
9 TraesCS7B01G014300 chr6A 57421391 57422580 1189 True 1838.000000 1838 94.583000 1365 2554 1 chr6A.!!$R1 1189
10 TraesCS7B01G014300 chr6A 527455237 527455779 542 False 893.000000 893 96.317000 3573 4115 1 chr6A.!!$F1 542
11 TraesCS7B01G014300 chr6B 360921789 360922870 1081 True 1676.000000 1676 94.516000 2813 3905 1 chr6B.!!$R1 1092
12 TraesCS7B01G014300 chr3D 34045231 34046468 1237 False 960.000000 1395 95.416500 1364 2558 2 chr3D.!!$F2 1194
13 TraesCS7B01G014300 chr3D 262775479 262776006 527 True 761.000000 761 92.655000 5 534 1 chr3D.!!$R1 529
14 TraesCS7B01G014300 chr3D 47284593 47285120 527 False 747.000000 747 92.135000 2 534 1 chr3D.!!$F1 532
15 TraesCS7B01G014300 chr2B 147618440 147619725 1285 True 917.500000 1363 93.579500 1363 2557 2 chr2B.!!$R1 1194
16 TraesCS7B01G014300 chr2B 147642023 147643264 1241 True 915.000000 1358 93.522500 1363 2557 2 chr2B.!!$R2 1194
17 TraesCS7B01G014300 chr7D 69041347 69048388 7041 False 827.200000 1203 92.359200 769 5731 5 chr7D.!!$F3 4962
18 TraesCS7B01G014300 chr7D 65936255 65940372 4117 True 741.333333 1271 91.498167 938 5840 6 chr7D.!!$R2 4902
19 TraesCS7B01G014300 chr7D 66347331 66348660 1329 True 589.500000 643 82.797000 630 3206 2 chr7D.!!$R3 2576
20 TraesCS7B01G014300 chr7A 6035822 6036577 755 False 1050.000000 1050 91.506000 3573 4349 1 chr7A.!!$F2 776
21 TraesCS7B01G014300 chr7A 5355390 5355954 564 False 911.000000 911 95.752000 1364 1928 1 chr7A.!!$F1 564
22 TraesCS7B01G014300 chr7A 74684195 74687697 3502 False 765.200000 1258 93.680400 536 5182 5 chr7A.!!$F5 4646
23 TraesCS7B01G014300 chr7A 70753926 70754457 531 True 525.000000 525 85.316000 855 1364 1 chr7A.!!$R1 509
24 TraesCS7B01G014300 chr7A 70733222 70737307 4085 True 521.375000 939 92.405375 851 5840 8 chr7A.!!$R4 4989
25 TraesCS7B01G014300 chr7A 70766339 70769552 3213 True 467.666667 778 87.593667 537 3206 3 chr7A.!!$R5 2669
26 TraesCS7B01G014300 chr7A 74697130 74697708 578 False 345.000000 534 96.459500 5182 5693 2 chr7A.!!$F6 511
27 TraesCS7B01G014300 chr3A 691450311 691451179 868 True 1022.000000 1022 88.128000 1363 2223 1 chr3A.!!$R1 860
28 TraesCS7B01G014300 chr1A 103030314 103031065 751 True 1018.000000 1018 90.874000 3573 4349 1 chr1A.!!$R1 776
29 TraesCS7B01G014300 chr1A 8508031 8508573 542 False 893.000000 893 96.317000 3573 4115 1 chr1A.!!$F1 542
30 TraesCS7B01G014300 chr4D 437895204 437895738 534 False 785.000000 785 93.135000 2 538 1 chr4D.!!$F1 536
31 TraesCS7B01G014300 chr2A 621519 622807 1288 True 586.666667 784 92.654333 1364 2555 3 chr2A.!!$R2 1191
32 TraesCS7B01G014300 chr1D 439692462 439692995 533 False 774.000000 774 92.910000 2 534 1 chr1D.!!$F1 532
33 TraesCS7B01G014300 chr1D 252515589 252516113 524 True 763.000000 763 92.844000 5 534 1 chr1D.!!$R2 529
34 TraesCS7B01G014300 chr2D 546255451 546255980 529 True 761.000000 761 92.523000 5 538 1 chr2D.!!$R1 533
35 TraesCS7B01G014300 chr6D 104446379 104446911 532 True 756.000000 756 92.193000 5 541 1 chr6D.!!$R1 536
36 TraesCS7B01G014300 chr6D 205895015 205895544 529 False 749.000000 749 92.135000 2 534 1 chr6D.!!$F1 532

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
999 2821 0.818040 AACCGTCTCAACCAACAGCC 60.818 55.0 0.00 0.00 0.00 4.85 F
1753 3698 0.398696 AACACGCCATCACACCCTTA 59.601 50.0 0.00 0.00 0.00 2.69 F
2204 4238 0.949397 ATACTTGCGGACGCTCGATA 59.051 50.0 18.04 5.75 42.51 2.92 F
2744 5810 0.034670 GCAGGAAGATGCTCTGGGTT 60.035 55.0 0.00 0.00 43.07 4.11 F
3411 6582 0.911769 TAGGAGGTCAACAGGCATGG 59.088 55.0 2.31 0.00 0.00 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2182 4213 1.069432 TCGAGCGTCCGCAAGTATATC 60.069 52.381 14.7 0.0 44.88 1.63 R
2684 4889 1.245376 TGTAGTCGATGGTGGCGTCA 61.245 55.000 0.0 0.0 0.00 4.35 R
3411 6582 2.376228 AAACCCAACCGGCACAATGC 62.376 55.000 0.0 0.0 44.08 3.56 R
4460 8154 1.146358 GGGCTCTTATGTCGTCGTGC 61.146 60.000 0.0 0.0 0.00 5.34 R
4856 8552 2.620367 GGGTGCATTAACCTGACCATGA 60.620 50.000 0.0 0.0 40.35 3.07 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
999 2821 0.818040 AACCGTCTCAACCAACAGCC 60.818 55.000 0.00 0.00 0.00 4.85
1062 2904 1.981495 CAAGAACCCACCTCTCCTTCT 59.019 52.381 0.00 0.00 0.00 2.85
1093 2935 3.749064 GCTCTCCAGCGTCACCGA 61.749 66.667 0.00 0.00 35.39 4.69
1309 3169 2.412323 CCACTACCTCGCCGCTACA 61.412 63.158 0.00 0.00 0.00 2.74
1312 3172 0.465824 ACTACCTCGCCGCTACAGAT 60.466 55.000 0.00 0.00 0.00 2.90
1689 3551 7.004225 CGTTTATTGAGTCGAACAAAGAAGAG 58.996 38.462 9.69 3.80 0.00 2.85
1751 3696 1.302511 GAACACGCCATCACACCCT 60.303 57.895 0.00 0.00 0.00 4.34
1753 3698 0.398696 AACACGCCATCACACCCTTA 59.601 50.000 0.00 0.00 0.00 2.69
1821 3766 7.541122 CCGTTTGGTTTTTCCTTTTAATCAA 57.459 32.000 0.00 0.00 37.07 2.57
2009 4031 4.631377 CCTCTTATTCAGACGAACATGCAA 59.369 41.667 0.00 0.00 32.81 4.08
2118 4146 2.224606 CAATCACGGCAAGGCTCATAT 58.775 47.619 0.00 0.00 0.00 1.78
2152 4180 1.009675 CCCATGCACGCGCTAAATC 60.010 57.895 5.73 0.00 39.64 2.17
2204 4238 0.949397 ATACTTGCGGACGCTCGATA 59.051 50.000 18.04 5.75 42.51 2.92
2362 4566 1.746171 CGACACCTCTCCGACATCCTA 60.746 57.143 0.00 0.00 0.00 2.94
2558 4763 3.591254 GACCGTGTCCACCCTGAGC 62.591 68.421 0.00 0.00 0.00 4.26
2684 4889 0.763223 ACGGGAGGTTCTGGAACACT 60.763 55.000 14.25 9.21 42.85 3.55
2694 4899 2.110213 GGAACACTGACGCCACCA 59.890 61.111 0.00 0.00 0.00 4.17
2744 5810 0.034670 GCAGGAAGATGCTCTGGGTT 60.035 55.000 0.00 0.00 43.07 4.11
2934 6079 3.970410 CTGCAGCTTCCCCACCCA 61.970 66.667 0.00 0.00 0.00 4.51
2995 6140 4.414956 TCGGGGGCCTCATCACCT 62.415 66.667 4.16 0.00 0.00 4.00
3085 6230 2.224066 CCCATGATAGACTTGGACGACC 60.224 54.545 0.00 0.00 43.75 4.79
3324 6469 8.504005 CGGTGTAGTCTGAAACTTTTGATAATT 58.496 33.333 0.00 0.00 39.55 1.40
3411 6582 0.911769 TAGGAGGTCAACAGGCATGG 59.088 55.000 2.31 0.00 0.00 3.66
3429 6600 2.866726 GCATTGTGCCGGTTGGGTT 61.867 57.895 1.90 0.00 37.42 4.11
3430 6601 1.745264 CATTGTGCCGGTTGGGTTT 59.255 52.632 1.90 0.00 38.44 3.27
3431 6602 0.962489 CATTGTGCCGGTTGGGTTTA 59.038 50.000 1.90 0.00 38.44 2.01
3432 6603 0.963225 ATTGTGCCGGTTGGGTTTAC 59.037 50.000 1.90 0.00 38.44 2.01
3433 6604 1.108132 TTGTGCCGGTTGGGTTTACC 61.108 55.000 1.90 0.00 38.44 2.85
3537 6708 5.182190 TGAATGTTGTTTGTAGTGTGTGTGT 59.818 36.000 0.00 0.00 0.00 3.72
3545 6716 1.466025 TAGTGTGTGTGTCGGGGGAC 61.466 60.000 0.00 0.00 0.00 4.46
3546 6717 3.918977 TGTGTGTGTCGGGGGACG 61.919 66.667 0.00 0.00 46.11 4.79
3778 7317 5.611374 ACTGTGCTTTAATACGATATGCCT 58.389 37.500 0.00 0.00 0.00 4.75
4128 7758 8.547967 TTTGATGGTACTATTCTTTGACTCAC 57.452 34.615 0.00 0.00 0.00 3.51
4130 7760 7.097192 TGATGGTACTATTCTTTGACTCACAC 58.903 38.462 0.00 0.00 0.00 3.82
4187 7817 1.906574 TGGTAGACTTCGGAGCCAATT 59.093 47.619 0.00 0.00 0.00 2.32
4683 8379 6.037940 GGCTACTACTTAATTGTTGTTAGCCC 59.962 42.308 11.80 0.00 37.02 5.19
4721 8417 4.974645 AGAACAGATGTGGTGGTTCTTA 57.025 40.909 0.00 0.00 45.52 2.10
4722 8418 5.304686 AGAACAGATGTGGTGGTTCTTAA 57.695 39.130 0.00 0.00 45.52 1.85
4726 8422 5.445964 ACAGATGTGGTGGTTCTTAAAGTT 58.554 37.500 0.00 0.00 0.00 2.66
4727 8423 5.891551 ACAGATGTGGTGGTTCTTAAAGTTT 59.108 36.000 0.00 0.00 0.00 2.66
4728 8424 6.379988 ACAGATGTGGTGGTTCTTAAAGTTTT 59.620 34.615 0.00 0.00 0.00 2.43
4729 8425 6.697019 CAGATGTGGTGGTTCTTAAAGTTTTG 59.303 38.462 0.00 0.00 0.00 2.44
4731 8427 6.347859 TGTGGTGGTTCTTAAAGTTTTGTT 57.652 33.333 0.00 0.00 0.00 2.83
4733 8429 8.068892 TGTGGTGGTTCTTAAAGTTTTGTTAT 57.931 30.769 0.00 0.00 0.00 1.89
4734 8430 8.532819 TGTGGTGGTTCTTAAAGTTTTGTTATT 58.467 29.630 0.00 0.00 0.00 1.40
4735 8431 9.027129 GTGGTGGTTCTTAAAGTTTTGTTATTC 57.973 33.333 0.00 0.00 0.00 1.75
4737 8433 7.380333 GGTGGTTCTTAAAGTTTTGTTATTCCG 59.620 37.037 0.00 0.00 0.00 4.30
4738 8434 6.919115 TGGTTCTTAAAGTTTTGTTATTCCGC 59.081 34.615 0.00 0.00 0.00 5.54
4739 8435 6.919115 GGTTCTTAAAGTTTTGTTATTCCGCA 59.081 34.615 0.00 0.00 0.00 5.69
4740 8436 7.597369 GGTTCTTAAAGTTTTGTTATTCCGCAT 59.403 33.333 0.00 0.00 0.00 4.73
4741 8437 9.615295 GTTCTTAAAGTTTTGTTATTCCGCATA 57.385 29.630 0.00 0.00 0.00 3.14
4742 8438 9.615295 TTCTTAAAGTTTTGTTATTCCGCATAC 57.385 29.630 0.00 0.00 0.00 2.39
4743 8439 8.784994 TCTTAAAGTTTTGTTATTCCGCATACA 58.215 29.630 0.00 0.00 0.00 2.29
4744 8440 8.730970 TTAAAGTTTTGTTATTCCGCATACAC 57.269 30.769 0.00 0.00 0.00 2.90
4745 8441 5.305139 AGTTTTGTTATTCCGCATACACC 57.695 39.130 0.00 0.00 0.00 4.16
4746 8442 4.762765 AGTTTTGTTATTCCGCATACACCA 59.237 37.500 0.00 0.00 0.00 4.17
4747 8443 5.417580 AGTTTTGTTATTCCGCATACACCAT 59.582 36.000 0.00 0.00 0.00 3.55
4748 8444 4.891627 TTGTTATTCCGCATACACCATG 57.108 40.909 0.00 0.00 37.73 3.66
4759 8455 4.659111 CATACACCATGCATGTTTGGAT 57.341 40.909 24.58 19.14 36.79 3.41
4760 8456 5.013568 CATACACCATGCATGTTTGGATT 57.986 39.130 24.58 8.68 36.79 3.01
4761 8457 5.421277 CATACACCATGCATGTTTGGATTT 58.579 37.500 24.58 8.37 36.79 2.17
4762 8458 4.354893 ACACCATGCATGTTTGGATTTT 57.645 36.364 24.58 3.34 36.79 1.82
4763 8459 5.480642 ACACCATGCATGTTTGGATTTTA 57.519 34.783 24.58 0.00 36.79 1.52
4764 8460 5.237048 ACACCATGCATGTTTGGATTTTAC 58.763 37.500 24.58 0.00 36.79 2.01
4765 8461 5.221601 ACACCATGCATGTTTGGATTTTACA 60.222 36.000 24.58 0.00 36.79 2.41
4766 8462 5.349270 CACCATGCATGTTTGGATTTTACAG 59.651 40.000 24.58 7.06 36.79 2.74
4767 8463 5.011943 ACCATGCATGTTTGGATTTTACAGT 59.988 36.000 24.58 7.68 36.79 3.55
4768 8464 6.210385 ACCATGCATGTTTGGATTTTACAGTA 59.790 34.615 24.58 0.00 36.79 2.74
4769 8465 7.093377 ACCATGCATGTTTGGATTTTACAGTAT 60.093 33.333 24.58 0.00 36.79 2.12
4770 8466 7.765360 CCATGCATGTTTGGATTTTACAGTATT 59.235 33.333 24.58 0.00 34.81 1.89
4771 8467 9.153721 CATGCATGTTTGGATTTTACAGTATTT 57.846 29.630 18.91 0.00 30.50 1.40
4772 8468 9.723601 ATGCATGTTTGGATTTTACAGTATTTT 57.276 25.926 0.00 0.00 28.01 1.82
4773 8469 9.202273 TGCATGTTTGGATTTTACAGTATTTTC 57.798 29.630 0.00 0.00 0.00 2.29
4774 8470 9.202273 GCATGTTTGGATTTTACAGTATTTTCA 57.798 29.630 0.00 0.00 0.00 2.69
4776 8472 9.705290 ATGTTTGGATTTTACAGTATTTTCACC 57.295 29.630 0.00 0.00 0.00 4.02
4777 8473 8.919145 TGTTTGGATTTTACAGTATTTTCACCT 58.081 29.630 0.00 0.00 0.00 4.00
4778 8474 9.191995 GTTTGGATTTTACAGTATTTTCACCTG 57.808 33.333 0.00 0.00 0.00 4.00
4856 8552 3.717576 TCATGGAGACCAGAGTTCTGAT 58.282 45.455 10.64 0.00 46.59 2.90
4920 8616 0.880718 TGCGTGCGTGGTGTATTTGA 60.881 50.000 0.00 0.00 0.00 2.69
4948 8644 0.319211 TACTTGCGTGCGTGTTAGCT 60.319 50.000 0.00 0.00 38.13 3.32
5038 8734 5.457799 GCACATTACATTGTTCATGAGCATC 59.542 40.000 13.38 0.00 36.24 3.91
5053 8749 4.392047 TGAGCATCACAACAACTTCAGAT 58.608 39.130 0.00 0.00 42.56 2.90
5057 8753 7.081526 AGCATCACAACAACTTCAGATATTC 57.918 36.000 0.00 0.00 0.00 1.75
5067 8763 9.566432 AACAACTTCAGATATTCTATGATTCCC 57.434 33.333 0.00 0.00 0.00 3.97
5071 8767 9.391227 ACTTCAGATATTCTATGATTCCCTCTT 57.609 33.333 0.00 0.00 0.00 2.85
5101 8797 6.367374 TGTCTCTTTCTCTCTCTGTCTCTA 57.633 41.667 0.00 0.00 0.00 2.43
5161 8857 9.743057 TTGAAGGTCAGTAAAAATGTATGTTTG 57.257 29.630 0.00 0.00 0.00 2.93
5162 8858 7.865385 TGAAGGTCAGTAAAAATGTATGTTTGC 59.135 33.333 0.00 0.00 0.00 3.68
5340 9041 8.508883 TGGAGTACTAATAAGACTCTTCACTC 57.491 38.462 0.00 0.00 39.66 3.51
5341 9042 7.556996 TGGAGTACTAATAAGACTCTTCACTCC 59.443 40.741 16.49 16.49 45.49 3.85
5465 16769 7.849804 TCAATCTCATTAAACTACTCCAAGC 57.150 36.000 0.00 0.00 0.00 4.01
5481 16785 0.896940 AAGCCATCAACCTGCCACAG 60.897 55.000 0.00 0.00 0.00 3.66
5483 16787 0.895100 GCCATCAACCTGCCACAGAA 60.895 55.000 0.00 0.00 32.44 3.02
5504 16808 6.260936 CAGAATGGTACTCACTTCTGTTTGTT 59.739 38.462 16.89 0.00 36.88 2.83
5663 17084 2.771943 TCACAACCACCTCTCTCTGTTT 59.228 45.455 0.00 0.00 0.00 2.83
5743 17164 1.067295 TTGTGCTGGGTGGAGATCTT 58.933 50.000 0.00 0.00 0.00 2.40
5779 17200 4.199432 AGAGTCGTTCAATGATGCTTCT 57.801 40.909 0.88 0.00 0.00 2.85
5780 17201 5.330455 AGAGTCGTTCAATGATGCTTCTA 57.670 39.130 0.88 0.00 0.00 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
999 2821 1.202245 CGGAGAAGAGAAGAAGCGAGG 60.202 57.143 0.00 0.00 0.00 4.63
1030 2852 0.313987 GGTTCTTGGTTTCTTGGCGG 59.686 55.000 0.00 0.00 0.00 6.13
1093 2935 0.247736 GGAACTGCTCCATCTGTCGT 59.752 55.000 0.00 0.00 44.67 4.34
1156 3007 3.411418 CTCGTCGGCGTGCAGGTAT 62.411 63.158 10.18 0.00 39.49 2.73
1306 3166 4.830765 GGCGCCGGCACATCTGTA 62.831 66.667 28.98 0.00 42.47 2.74
1689 3551 1.935065 CTCACGCGCGACTTGAGTTC 61.935 60.000 39.36 0.00 39.28 3.01
1751 3696 6.127054 CCCCTGTGTGACTCTCAGATAATTAA 60.127 42.308 7.89 0.00 39.24 1.40
1753 3698 4.163078 CCCCTGTGTGACTCTCAGATAATT 59.837 45.833 7.89 0.00 39.24 1.40
1852 3797 8.171196 CCTAAATTATCGGATCGAATCATGTTG 58.829 37.037 0.00 0.00 39.99 3.33
2118 4146 3.704545 ATGGGCCCATGATTTTCCTTA 57.295 42.857 37.06 3.84 35.03 2.69
2152 4180 1.850377 TTTTCCGTTGCATGCAAGTG 58.150 45.000 32.64 25.69 36.52 3.16
2182 4213 1.069432 TCGAGCGTCCGCAAGTATATC 60.069 52.381 14.70 0.00 44.88 1.63
2362 4566 2.034687 GTCACTGCATGTGGGCCT 59.965 61.111 4.53 0.00 46.20 5.19
2497 4702 4.143333 CCGTCGATTGGACCGGCT 62.143 66.667 0.00 0.00 42.99 5.52
2558 4763 2.619177 CACCTCAGGATGGTAGTAGTCG 59.381 54.545 0.00 0.00 35.80 4.18
2610 4815 3.032459 GGTAGACCTCTTCCTCGGATTT 58.968 50.000 0.00 0.00 31.55 2.17
2684 4889 1.245376 TGTAGTCGATGGTGGCGTCA 61.245 55.000 0.00 0.00 0.00 4.35
2694 4899 2.619177 CGAGGTCCTCAATGTAGTCGAT 59.381 50.000 19.15 0.00 0.00 3.59
2934 6079 2.435938 ATCCGCGACCGCAACATT 60.436 55.556 8.23 0.00 42.06 2.71
2995 6140 3.033764 GAACACGAACGAGCCGCA 61.034 61.111 0.14 0.00 0.00 5.69
3085 6230 4.899239 GCCCATGACGAGCTCGGG 62.899 72.222 36.93 28.01 44.95 5.14
3218 6363 3.503748 CGAGTTTCTTGCCAAAGGAGAAT 59.496 43.478 0.00 0.00 33.90 2.40
3411 6582 2.376228 AAACCCAACCGGCACAATGC 62.376 55.000 0.00 0.00 44.08 3.56
3429 6600 4.648762 TCCGACTATTCCCATAAACGGTAA 59.351 41.667 0.00 0.00 36.17 2.85
3430 6601 4.214310 TCCGACTATTCCCATAAACGGTA 58.786 43.478 0.00 0.00 36.17 4.02
3431 6602 3.033184 TCCGACTATTCCCATAAACGGT 58.967 45.455 0.00 0.00 36.17 4.83
3432 6603 3.738830 TCCGACTATTCCCATAAACGG 57.261 47.619 0.00 0.00 36.12 4.44
3433 6604 4.506654 CAGTTCCGACTATTCCCATAAACG 59.493 45.833 0.00 0.00 33.90 3.60
3434 6605 4.272748 GCAGTTCCGACTATTCCCATAAAC 59.727 45.833 0.00 0.00 33.90 2.01
3435 6606 4.080807 TGCAGTTCCGACTATTCCCATAAA 60.081 41.667 0.00 0.00 33.90 1.40
3778 7317 4.657814 AATTCCAAAGCCTTCCACTAGA 57.342 40.909 0.00 0.00 0.00 2.43
4115 7745 9.512588 AGAAATGAATAGTGTGAGTCAAAGAAT 57.487 29.630 0.00 0.00 0.00 2.40
4460 8154 1.146358 GGGCTCTTATGTCGTCGTGC 61.146 60.000 0.00 0.00 0.00 5.34
4721 8417 6.153756 GGTGTATGCGGAATAACAAAACTTT 58.846 36.000 0.00 0.00 0.00 2.66
4722 8418 5.241949 TGGTGTATGCGGAATAACAAAACTT 59.758 36.000 0.00 0.00 0.00 2.66
4726 8422 5.242069 CATGGTGTATGCGGAATAACAAA 57.758 39.130 0.00 0.00 0.00 2.83
4727 8423 4.891627 CATGGTGTATGCGGAATAACAA 57.108 40.909 0.00 0.00 0.00 2.83
4738 8434 4.659111 ATCCAAACATGCATGGTGTATG 57.341 40.909 29.41 18.41 44.44 2.39
4739 8435 5.680594 AAATCCAAACATGCATGGTGTAT 57.319 34.783 29.41 16.34 37.94 2.29
4740 8436 5.480642 AAAATCCAAACATGCATGGTGTA 57.519 34.783 29.41 14.85 37.94 2.90
4741 8437 4.354893 AAAATCCAAACATGCATGGTGT 57.645 36.364 29.41 12.37 37.94 4.16
4742 8438 5.236282 TGTAAAATCCAAACATGCATGGTG 58.764 37.500 29.41 24.27 37.94 4.17
4743 8439 5.011943 ACTGTAAAATCCAAACATGCATGGT 59.988 36.000 29.41 22.35 37.94 3.55
4744 8440 5.481105 ACTGTAAAATCCAAACATGCATGG 58.519 37.500 29.41 14.60 38.09 3.66
4745 8441 8.706492 AATACTGTAAAATCCAAACATGCATG 57.294 30.769 25.09 25.09 0.00 4.06
4746 8442 9.723601 AAAATACTGTAAAATCCAAACATGCAT 57.276 25.926 0.00 0.00 0.00 3.96
4747 8443 9.202273 GAAAATACTGTAAAATCCAAACATGCA 57.798 29.630 0.00 0.00 0.00 3.96
4748 8444 9.202273 TGAAAATACTGTAAAATCCAAACATGC 57.798 29.630 0.00 0.00 0.00 4.06
4750 8446 9.705290 GGTGAAAATACTGTAAAATCCAAACAT 57.295 29.630 0.00 0.00 0.00 2.71
4751 8447 8.919145 AGGTGAAAATACTGTAAAATCCAAACA 58.081 29.630 0.00 0.00 0.00 2.83
4752 8448 9.191995 CAGGTGAAAATACTGTAAAATCCAAAC 57.808 33.333 0.00 0.00 0.00 2.93
4753 8449 8.919145 ACAGGTGAAAATACTGTAAAATCCAAA 58.081 29.630 0.00 0.00 43.13 3.28
4754 8450 8.472007 ACAGGTGAAAATACTGTAAAATCCAA 57.528 30.769 0.00 0.00 43.13 3.53
4755 8451 8.356657 CAACAGGTGAAAATACTGTAAAATCCA 58.643 33.333 0.00 0.00 44.08 3.41
4756 8452 8.573035 TCAACAGGTGAAAATACTGTAAAATCC 58.427 33.333 0.00 0.00 44.08 3.01
4757 8453 9.612620 CTCAACAGGTGAAAATACTGTAAAATC 57.387 33.333 0.00 0.00 44.08 2.17
4758 8454 9.131791 ACTCAACAGGTGAAAATACTGTAAAAT 57.868 29.630 0.00 0.00 44.08 1.82
4759 8455 8.514330 ACTCAACAGGTGAAAATACTGTAAAA 57.486 30.769 0.00 0.00 44.08 1.52
4760 8456 8.514330 AACTCAACAGGTGAAAATACTGTAAA 57.486 30.769 0.00 0.00 44.08 2.01
4761 8457 8.514330 AAACTCAACAGGTGAAAATACTGTAA 57.486 30.769 0.00 0.00 44.08 2.41
4762 8458 8.402472 CAAAACTCAACAGGTGAAAATACTGTA 58.598 33.333 0.00 0.00 44.08 2.74
4763 8459 7.093945 ACAAAACTCAACAGGTGAAAATACTGT 60.094 33.333 0.00 0.00 46.59 3.55
4764 8460 7.257722 ACAAAACTCAACAGGTGAAAATACTG 58.742 34.615 0.00 0.00 35.22 2.74
4765 8461 7.404671 ACAAAACTCAACAGGTGAAAATACT 57.595 32.000 0.00 0.00 35.22 2.12
4766 8462 9.744468 ATAACAAAACTCAACAGGTGAAAATAC 57.256 29.630 0.00 0.00 35.22 1.89
4768 8464 9.313118 GAATAACAAAACTCAACAGGTGAAAAT 57.687 29.630 0.00 0.00 35.22 1.82
4769 8465 7.762159 GGAATAACAAAACTCAACAGGTGAAAA 59.238 33.333 0.00 0.00 35.22 2.29
4770 8466 7.262048 GGAATAACAAAACTCAACAGGTGAAA 58.738 34.615 0.00 0.00 35.22 2.69
4771 8467 6.459024 CGGAATAACAAAACTCAACAGGTGAA 60.459 38.462 0.00 0.00 35.22 3.18
4772 8468 5.008217 CGGAATAACAAAACTCAACAGGTGA 59.992 40.000 0.00 0.00 34.17 4.02
4773 8469 5.212194 CGGAATAACAAAACTCAACAGGTG 58.788 41.667 0.00 0.00 0.00 4.00
4774 8470 4.261447 GCGGAATAACAAAACTCAACAGGT 60.261 41.667 0.00 0.00 0.00 4.00
4775 8471 4.023193 AGCGGAATAACAAAACTCAACAGG 60.023 41.667 0.00 0.00 0.00 4.00
4776 8472 5.108385 AGCGGAATAACAAAACTCAACAG 57.892 39.130 0.00 0.00 0.00 3.16
4777 8473 5.508200 AAGCGGAATAACAAAACTCAACA 57.492 34.783 0.00 0.00 0.00 3.33
4778 8474 7.646526 ACTTTAAGCGGAATAACAAAACTCAAC 59.353 33.333 0.00 0.00 0.00 3.18
4856 8552 2.620367 GGGTGCATTAACCTGACCATGA 60.620 50.000 0.00 0.00 40.35 3.07
5057 8753 7.512992 AGACATAAACCAAGAGGGAATCATAG 58.487 38.462 0.00 0.00 41.15 2.23
5062 8758 6.394345 AAGAGACATAAACCAAGAGGGAAT 57.606 37.500 0.00 0.00 41.15 3.01
5067 8763 7.610865 AGAGAGAAAGAGACATAAACCAAGAG 58.389 38.462 0.00 0.00 0.00 2.85
5071 8767 6.495181 ACAGAGAGAGAAAGAGACATAAACCA 59.505 38.462 0.00 0.00 0.00 3.67
5077 8773 5.819991 AGAGACAGAGAGAGAAAGAGACAT 58.180 41.667 0.00 0.00 0.00 3.06
5126 8822 9.883142 ATTTTTACTGACCTTCAAATGTTTCAA 57.117 25.926 0.00 0.00 0.00 2.69
5300 9000 6.552445 AGTACTCCATAAGATTGCAGAGTT 57.448 37.500 6.33 0.00 36.14 3.01
5465 16769 1.475280 CATTCTGTGGCAGGTTGATGG 59.525 52.381 0.00 0.00 31.51 3.51
5481 16785 6.619801 AACAAACAGAAGTGAGTACCATTC 57.380 37.500 0.00 0.00 0.00 2.67
5483 16787 8.691661 AATTAACAAACAGAAGTGAGTACCAT 57.308 30.769 0.00 0.00 0.00 3.55
5511 16815 6.760440 ATGTATCTCATTCCTTGATCACCT 57.240 37.500 0.00 0.00 32.72 4.00


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

AutoCloner maintained by Alex Coulton.