Multiple sequence alignment - TraesCS7D01G330500

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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 TraesCS7D01G330500 chr7D 100.000 2600 0 0 1 2600 422152081 422154680 0.000000e+00 4802.0
1 TraesCS7D01G330500 chr7D 90.751 1092 59 13 818 1888 525766030 525764960 0.000000e+00 1419.0
2 TraesCS7D01G330500 chr7D 82.662 1217 146 51 714 1886 505349170 505350365 0.000000e+00 1018.0
3 TraesCS7D01G330500 chr7D 82.845 921 120 28 720 1622 599719424 599718524 0.000000e+00 791.0
4 TraesCS7D01G330500 chr7D 79.936 628 67 34 93 703 587149838 587150423 8.660000e-110 407.0
5 TraesCS7D01G330500 chr7D 90.385 52 4 1 2540 2591 567477145 567477195 1.670000e-07 67.6
6 TraesCS7D01G330500 chr4D 90.512 1212 71 15 711 1886 224752805 224754008 0.000000e+00 1561.0
7 TraesCS7D01G330500 chr4D 91.773 1094 60 12 817 1886 53419405 53420492 0.000000e+00 1495.0
8 TraesCS7D01G330500 chr4D 83.721 688 72 27 1236 1891 489629607 489628928 4.760000e-172 614.0
9 TraesCS7D01G330500 chr7A 91.182 1100 59 13 819 1888 15255109 15256200 0.000000e+00 1459.0
10 TraesCS7D01G330500 chr7A 87.193 734 44 14 1 709 511012682 511011974 0.000000e+00 789.0
11 TraesCS7D01G330500 chr5A 88.550 1214 91 18 713 1886 631680098 631681303 0.000000e+00 1428.0
12 TraesCS7D01G330500 chr5A 86.213 1204 117 30 713 1886 709279702 709280886 0.000000e+00 1258.0
13 TraesCS7D01G330500 chr5A 85.482 737 44 25 1 711 537369456 537368757 0.000000e+00 710.0
14 TraesCS7D01G330500 chr5D 91.563 1043 57 11 868 1888 370953311 370954344 0.000000e+00 1410.0
15 TraesCS7D01G330500 chr5D 91.753 970 57 6 817 1774 499061021 499061979 0.000000e+00 1327.0
16 TraesCS7D01G330500 chr5D 90.231 737 28 16 1178 1885 524593267 524593988 0.000000e+00 922.0
17 TraesCS7D01G330500 chr5D 80.362 1217 173 42 716 1889 424819147 424820340 0.000000e+00 863.0
18 TraesCS7D01G330500 chr5D 85.948 733 42 26 1 710 423965103 423964409 0.000000e+00 726.0
19 TraesCS7D01G330500 chr5D 83.283 329 18 17 271 587 562708948 562709251 4.260000e-68 268.0
20 TraesCS7D01G330500 chr5D 93.617 47 3 0 2540 2586 538262620 538262574 1.290000e-08 71.3
21 TraesCS7D01G330500 chr2A 88.240 1199 94 14 713 1867 760865948 760864753 0.000000e+00 1389.0
22 TraesCS7D01G330500 chr2A 87.971 1222 85 26 716 1888 744777489 744776281 0.000000e+00 1386.0
23 TraesCS7D01G330500 chr2A 89.039 1113 74 15 817 1884 22846671 22845562 0.000000e+00 1336.0
24 TraesCS7D01G330500 chr2A 88.847 1049 69 17 715 1737 206898273 206899299 0.000000e+00 1245.0
25 TraesCS7D01G330500 chr2A 84.268 1106 129 31 808 1886 723575585 723576672 0.000000e+00 1037.0
26 TraesCS7D01G330500 chr2A 81.346 1233 139 49 711 1891 10984923 10986116 0.000000e+00 918.0
27 TraesCS7D01G330500 chr2A 92.308 39 0 2 2091 2129 89934308 89934343 5.000000e-03 52.8
28 TraesCS7D01G330500 chrUn 89.327 1115 70 14 817 1884 154152312 154151200 0.000000e+00 1354.0
29 TraesCS7D01G330500 chrUn 88.809 1117 74 14 817 1884 146971420 146970306 0.000000e+00 1323.0
30 TraesCS7D01G330500 chrUn 86.769 1232 83 26 713 1886 146942426 146943635 0.000000e+00 1299.0
31 TraesCS7D01G330500 chr3D 81.611 1229 156 44 721 1892 545438668 545437453 0.000000e+00 953.0
32 TraesCS7D01G330500 chr3D 92.000 50 2 2 2540 2587 308792334 308792285 4.640000e-08 69.4
33 TraesCS7D01G330500 chr7B 93.186 587 23 4 1 584 438951014 438950442 0.000000e+00 846.0
34 TraesCS7D01G330500 chr7B 85.315 715 50 22 1931 2600 438949685 438948981 0.000000e+00 688.0
35 TraesCS7D01G330500 chr7B 79.444 647 71 31 87 711 658267979 658268585 4.030000e-108 401.0
36 TraesCS7D01G330500 chr7B 96.190 105 2 2 586 689 438950072 438949969 1.240000e-38 171.0
37 TraesCS7D01G330500 chr3B 79.641 1169 170 41 759 1888 22890842 22889703 0.000000e+00 778.0
38 TraesCS7D01G330500 chr1D 79.282 1226 156 64 713 1891 236091252 236090078 0.000000e+00 767.0
39 TraesCS7D01G330500 chr1D 92.000 50 3 1 2540 2589 470945319 470945271 4.640000e-08 69.4
40 TraesCS7D01G330500 chr5B 85.873 722 37 17 11 711 511835893 511835216 0.000000e+00 708.0
41 TraesCS7D01G330500 chr6A 81.284 732 66 43 19 711 49551303 49550604 6.370000e-146 527.0
42 TraesCS7D01G330500 chr6A 78.738 729 52 57 19 711 49484218 49483557 2.430000e-105 392.0
43 TraesCS7D01G330500 chr6A 78.363 721 54 48 19 711 49197202 49196556 8.790000e-100 374.0
44 TraesCS7D01G330500 chr6A 78.501 707 53 46 19 687 49500180 49499535 3.160000e-99 372.0
45 TraesCS7D01G330500 chr6A 79.566 553 51 31 19 547 49202484 49201970 3.200000e-89 339.0
46 TraesCS7D01G330500 chr6A 90.278 72 6 1 638 709 49201647 49201577 2.750000e-15 93.5
47 TraesCS7D01G330500 chr6B 81.492 697 58 40 19 682 88736541 88735883 8.300000e-140 507.0
48 TraesCS7D01G330500 chr6B 79.277 719 71 31 12 711 88781762 88781103 5.140000e-117 431.0
49 TraesCS7D01G330500 chr6B 79.526 591 49 30 19 587 88717881 88717341 3.180000e-94 355.0
50 TraesCS7D01G330500 chr6B 93.878 49 2 1 2540 2587 55433078 55433126 3.590000e-09 73.1
51 TraesCS7D01G330500 chr6D 80.495 728 63 37 19 711 37934477 37933794 3.890000e-133 484.0
52 TraesCS7D01G330500 chr6D 79.809 733 72 44 19 709 37928246 37927548 5.070000e-127 464.0
53 TraesCS7D01G330500 chr6D 79.545 704 59 38 19 691 38120283 38119634 8.600000e-115 424.0
54 TraesCS7D01G330500 chr2B 80.549 401 43 17 1508 1888 626654030 626653645 2.550000e-70 276.0
55 TraesCS7D01G330500 chr4B 91.813 171 7 3 3 169 4232352 4232185 5.600000e-57 231.0
56 TraesCS7D01G330500 chr4A 92.025 163 10 1 7 169 663652491 663652650 2.600000e-55 226.0
57 TraesCS7D01G330500 chr3A 93.878 49 2 1 2539 2587 428413336 428413289 3.590000e-09 73.1
58 TraesCS7D01G330500 chr1B 93.617 47 2 1 2540 2585 619395888 619395842 4.640000e-08 69.4
59 TraesCS7D01G330500 chr1B 93.617 47 2 1 2540 2586 624023441 624023486 4.640000e-08 69.4


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 TraesCS7D01G330500 chr7D 422152081 422154680 2599 False 4802.000000 4802 100.000000 1 2600 1 chr7D.!!$F1 2599
1 TraesCS7D01G330500 chr7D 525764960 525766030 1070 True 1419.000000 1419 90.751000 818 1888 1 chr7D.!!$R1 1070
2 TraesCS7D01G330500 chr7D 505349170 505350365 1195 False 1018.000000 1018 82.662000 714 1886 1 chr7D.!!$F2 1172
3 TraesCS7D01G330500 chr7D 599718524 599719424 900 True 791.000000 791 82.845000 720 1622 1 chr7D.!!$R2 902
4 TraesCS7D01G330500 chr7D 587149838 587150423 585 False 407.000000 407 79.936000 93 703 1 chr7D.!!$F4 610
5 TraesCS7D01G330500 chr4D 224752805 224754008 1203 False 1561.000000 1561 90.512000 711 1886 1 chr4D.!!$F2 1175
6 TraesCS7D01G330500 chr4D 53419405 53420492 1087 False 1495.000000 1495 91.773000 817 1886 1 chr4D.!!$F1 1069
7 TraesCS7D01G330500 chr4D 489628928 489629607 679 True 614.000000 614 83.721000 1236 1891 1 chr4D.!!$R1 655
8 TraesCS7D01G330500 chr7A 15255109 15256200 1091 False 1459.000000 1459 91.182000 819 1888 1 chr7A.!!$F1 1069
9 TraesCS7D01G330500 chr7A 511011974 511012682 708 True 789.000000 789 87.193000 1 709 1 chr7A.!!$R1 708
10 TraesCS7D01G330500 chr5A 631680098 631681303 1205 False 1428.000000 1428 88.550000 713 1886 1 chr5A.!!$F1 1173
11 TraesCS7D01G330500 chr5A 709279702 709280886 1184 False 1258.000000 1258 86.213000 713 1886 1 chr5A.!!$F2 1173
12 TraesCS7D01G330500 chr5A 537368757 537369456 699 True 710.000000 710 85.482000 1 711 1 chr5A.!!$R1 710
13 TraesCS7D01G330500 chr5D 370953311 370954344 1033 False 1410.000000 1410 91.563000 868 1888 1 chr5D.!!$F1 1020
14 TraesCS7D01G330500 chr5D 499061021 499061979 958 False 1327.000000 1327 91.753000 817 1774 1 chr5D.!!$F3 957
15 TraesCS7D01G330500 chr5D 524593267 524593988 721 False 922.000000 922 90.231000 1178 1885 1 chr5D.!!$F4 707
16 TraesCS7D01G330500 chr5D 424819147 424820340 1193 False 863.000000 863 80.362000 716 1889 1 chr5D.!!$F2 1173
17 TraesCS7D01G330500 chr5D 423964409 423965103 694 True 726.000000 726 85.948000 1 710 1 chr5D.!!$R1 709
18 TraesCS7D01G330500 chr2A 760864753 760865948 1195 True 1389.000000 1389 88.240000 713 1867 1 chr2A.!!$R3 1154
19 TraesCS7D01G330500 chr2A 744776281 744777489 1208 True 1386.000000 1386 87.971000 716 1888 1 chr2A.!!$R2 1172
20 TraesCS7D01G330500 chr2A 22845562 22846671 1109 True 1336.000000 1336 89.039000 817 1884 1 chr2A.!!$R1 1067
21 TraesCS7D01G330500 chr2A 206898273 206899299 1026 False 1245.000000 1245 88.847000 715 1737 1 chr2A.!!$F3 1022
22 TraesCS7D01G330500 chr2A 723575585 723576672 1087 False 1037.000000 1037 84.268000 808 1886 1 chr2A.!!$F4 1078
23 TraesCS7D01G330500 chr2A 10984923 10986116 1193 False 918.000000 918 81.346000 711 1891 1 chr2A.!!$F1 1180
24 TraesCS7D01G330500 chrUn 154151200 154152312 1112 True 1354.000000 1354 89.327000 817 1884 1 chrUn.!!$R2 1067
25 TraesCS7D01G330500 chrUn 146970306 146971420 1114 True 1323.000000 1323 88.809000 817 1884 1 chrUn.!!$R1 1067
26 TraesCS7D01G330500 chrUn 146942426 146943635 1209 False 1299.000000 1299 86.769000 713 1886 1 chrUn.!!$F1 1173
27 TraesCS7D01G330500 chr3D 545437453 545438668 1215 True 953.000000 953 81.611000 721 1892 1 chr3D.!!$R2 1171
28 TraesCS7D01G330500 chr7B 438948981 438951014 2033 True 568.333333 846 91.563667 1 2600 3 chr7B.!!$R1 2599
29 TraesCS7D01G330500 chr7B 658267979 658268585 606 False 401.000000 401 79.444000 87 711 1 chr7B.!!$F1 624
30 TraesCS7D01G330500 chr3B 22889703 22890842 1139 True 778.000000 778 79.641000 759 1888 1 chr3B.!!$R1 1129
31 TraesCS7D01G330500 chr1D 236090078 236091252 1174 True 767.000000 767 79.282000 713 1891 1 chr1D.!!$R1 1178
32 TraesCS7D01G330500 chr5B 511835216 511835893 677 True 708.000000 708 85.873000 11 711 1 chr5B.!!$R1 700
33 TraesCS7D01G330500 chr6A 49550604 49551303 699 True 527.000000 527 81.284000 19 711 1 chr6A.!!$R4 692
34 TraesCS7D01G330500 chr6A 49483557 49484218 661 True 392.000000 392 78.738000 19 711 1 chr6A.!!$R2 692
35 TraesCS7D01G330500 chr6A 49196556 49197202 646 True 374.000000 374 78.363000 19 711 1 chr6A.!!$R1 692
36 TraesCS7D01G330500 chr6A 49499535 49500180 645 True 372.000000 372 78.501000 19 687 1 chr6A.!!$R3 668
37 TraesCS7D01G330500 chr6A 49201577 49202484 907 True 216.250000 339 84.922000 19 709 2 chr6A.!!$R5 690
38 TraesCS7D01G330500 chr6B 88735883 88736541 658 True 507.000000 507 81.492000 19 682 1 chr6B.!!$R2 663
39 TraesCS7D01G330500 chr6B 88781103 88781762 659 True 431.000000 431 79.277000 12 711 1 chr6B.!!$R3 699
40 TraesCS7D01G330500 chr6B 88717341 88717881 540 True 355.000000 355 79.526000 19 587 1 chr6B.!!$R1 568
41 TraesCS7D01G330500 chr6D 37933794 37934477 683 True 484.000000 484 80.495000 19 711 1 chr6D.!!$R2 692
42 TraesCS7D01G330500 chr6D 37927548 37928246 698 True 464.000000 464 79.809000 19 709 1 chr6D.!!$R1 690
43 TraesCS7D01G330500 chr6D 38119634 38120283 649 True 424.000000 424 79.545000 19 691 1 chr6D.!!$R3 672

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
342 398 0.173481 TGACAGCTACGCCATGACTC 59.827 55.0 0.0 0.0 0.0 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2139 2879 1.939934 CACTGGAAGAGTTCACGCAAA 59.06 47.619 0.0 0.0 37.43 3.68 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
140 172 2.203139 CAGTGCAACACCACCGGA 60.203 61.111 9.46 0.00 41.43 5.14
312 365 3.452786 CTCCCGAGCCGCTTCAGA 61.453 66.667 0.00 0.00 0.00 3.27
335 391 2.202810 GCTCCTGACAGCTACGCC 60.203 66.667 0.00 0.00 36.38 5.68
336 392 3.006756 GCTCCTGACAGCTACGCCA 62.007 63.158 0.00 0.00 36.38 5.69
337 393 1.819229 CTCCTGACAGCTACGCCAT 59.181 57.895 0.00 0.00 0.00 4.40
338 394 0.529337 CTCCTGACAGCTACGCCATG 60.529 60.000 0.00 0.00 0.00 3.66
339 395 0.970427 TCCTGACAGCTACGCCATGA 60.970 55.000 0.00 0.00 0.00 3.07
340 396 0.807667 CCTGACAGCTACGCCATGAC 60.808 60.000 0.00 0.00 0.00 3.06
341 397 0.174389 CTGACAGCTACGCCATGACT 59.826 55.000 0.00 0.00 0.00 3.41
342 398 0.173481 TGACAGCTACGCCATGACTC 59.827 55.000 0.00 0.00 0.00 3.36
443 508 1.408702 GAAGAAGATCTGCCGCTCTCT 59.591 52.381 0.00 0.00 0.00 3.10
521 600 2.105649 GGGACTGGAAGGATCTTCCATC 59.894 54.545 24.30 21.34 46.47 3.51
605 1062 2.236959 GAGAGGAGTGGGAGGGAGCT 62.237 65.000 0.00 0.00 0.00 4.09
746 1245 2.666344 CGCGGTAACTTGGTTTTTAGCC 60.666 50.000 0.00 0.00 0.00 3.93
750 1249 3.319689 GGTAACTTGGTTTTTAGCCTGCA 59.680 43.478 0.00 0.00 0.00 4.41
797 1313 1.644786 GGCTGGAAATAAGCGCACGT 61.645 55.000 11.47 0.00 41.78 4.49
799 1315 1.075542 CTGGAAATAAGCGCACGTGA 58.924 50.000 22.23 0.00 0.00 4.35
801 1317 1.874231 TGGAAATAAGCGCACGTGAAA 59.126 42.857 22.23 0.00 0.00 2.69
804 1320 3.917985 GGAAATAAGCGCACGTGAAAAAT 59.082 39.130 22.23 2.26 0.00 1.82
805 1321 5.090083 GGAAATAAGCGCACGTGAAAAATA 58.910 37.500 22.23 5.37 0.00 1.40
806 1322 5.569823 GGAAATAAGCGCACGTGAAAAATAA 59.430 36.000 22.23 0.00 0.00 1.40
807 1323 6.252655 GGAAATAAGCGCACGTGAAAAATAAT 59.747 34.615 22.23 0.00 0.00 1.28
808 1324 7.201401 GGAAATAAGCGCACGTGAAAAATAATT 60.201 33.333 22.23 6.46 0.00 1.40
809 1325 4.884257 AAGCGCACGTGAAAAATAATTG 57.116 36.364 22.23 0.00 0.00 2.32
810 1326 2.661195 AGCGCACGTGAAAAATAATTGC 59.339 40.909 22.23 6.24 0.00 3.56
811 1327 3.253747 CGCACGTGAAAAATAATTGCG 57.746 42.857 22.23 7.02 44.44 4.85
812 1328 2.530065 CGCACGTGAAAAATAATTGCGC 60.530 45.455 22.23 0.00 43.98 6.09
813 1329 2.530065 GCACGTGAAAAATAATTGCGCG 60.530 45.455 22.23 0.00 35.25 6.86
814 1330 2.654528 CACGTGAAAAATAATTGCGCGT 59.345 40.909 10.90 2.12 39.72 6.01
815 1331 2.906161 ACGTGAAAAATAATTGCGCGTC 59.094 40.909 8.43 0.00 36.68 5.19
1491 2056 1.619654 CTCAAAATGGTGGGCAGACA 58.380 50.000 0.00 0.00 0.00 3.41
1529 2096 1.270625 TGACCGTTGGAAGGACATGTC 60.271 52.381 17.91 17.91 0.00 3.06
1558 2134 3.062466 CGGACCAGACCAGCGAGA 61.062 66.667 0.00 0.00 0.00 4.04
1950 2671 2.504367 AGAGTGCATTTTGCTAACCGT 58.496 42.857 0.00 0.00 45.31 4.83
1959 2680 2.048503 GCTAACCGTCGCACACCT 60.049 61.111 0.00 0.00 0.00 4.00
1963 2684 2.758770 TAACCGTCGCACACCTGCTC 62.759 60.000 0.00 0.00 41.77 4.26
2053 2784 7.845617 TTTATCAAATTCGTGAAACTTTCCG 57.154 32.000 0.00 3.22 31.75 4.30
2054 2785 3.623863 TCAAATTCGTGAAACTTTCCGC 58.376 40.909 0.00 0.00 31.75 5.54
2061 2800 5.171147 TCGTGAAACTTTCCGCATTTTTA 57.829 34.783 0.00 0.00 31.75 1.52
2070 2809 7.561021 ACTTTCCGCATTTTTACCAAATTTT 57.439 28.000 0.00 0.00 0.00 1.82
2076 2815 8.889717 TCCGCATTTTTACCAAATTTTAAAACA 58.110 25.926 1.97 2.18 29.06 2.83
2116 2856 7.656948 TGAACCTTTCATTTCAAATCCATGAAC 59.343 33.333 0.00 0.00 36.80 3.18
2123 2863 9.835389 TTCATTTCAAATCCATGAACTTTTTCT 57.165 25.926 0.00 0.00 38.95 2.52
2127 2867 9.664332 TTTCAAATCCATGAACTTTTTCTCAAA 57.336 25.926 0.00 0.00 38.95 2.69
2129 2869 9.263538 TCAAATCCATGAACTTTTTCTCAAATG 57.736 29.630 0.00 0.00 32.36 2.32
2130 2870 7.662604 AATCCATGAACTTTTTCTCAAATGC 57.337 32.000 0.00 0.00 32.36 3.56
2131 2871 5.221880 TCCATGAACTTTTTCTCAAATGCG 58.778 37.500 0.00 0.00 32.36 4.73
2133 2873 5.463061 CCATGAACTTTTTCTCAAATGCGTT 59.537 36.000 0.00 0.00 32.36 4.84
2136 2876 8.702438 CATGAACTTTTTCTCAAATGCGTTAAT 58.298 29.630 0.00 0.00 32.36 1.40
2137 2877 8.641499 TGAACTTTTTCTCAAATGCGTTAATT 57.359 26.923 0.00 0.00 32.36 1.40
2138 2878 9.092876 TGAACTTTTTCTCAAATGCGTTAATTT 57.907 25.926 0.00 0.00 32.36 1.82
2139 2879 9.914923 GAACTTTTTCTCAAATGCGTTAATTTT 57.085 25.926 0.00 0.00 0.00 1.82
2157 2897 3.691049 TTTTTGCGTGAACTCTTCCAG 57.309 42.857 0.00 0.00 0.00 3.86
2158 2898 2.325583 TTTGCGTGAACTCTTCCAGT 57.674 45.000 0.00 0.00 36.64 4.00
2159 2899 1.581934 TTGCGTGAACTCTTCCAGTG 58.418 50.000 0.00 0.00 34.56 3.66
2160 2900 0.750249 TGCGTGAACTCTTCCAGTGA 59.250 50.000 0.00 0.00 34.56 3.41
2161 2901 1.344438 TGCGTGAACTCTTCCAGTGAT 59.656 47.619 0.00 0.00 34.56 3.06
2163 2903 3.006430 TGCGTGAACTCTTCCAGTGATTA 59.994 43.478 0.00 0.00 34.56 1.75
2219 2959 7.525759 TGTGAGTTTTCTTTTCCAAATTTTGC 58.474 30.769 3.50 0.00 0.00 3.68
2223 2963 7.811653 AGTTTTCTTTTCCAAATTTTGCGAAA 58.188 26.923 15.67 15.67 32.13 3.46
2401 3143 7.227992 TGTTTTAACCTTTTTGAATCTTGCG 57.772 32.000 0.00 0.00 0.00 4.85
2409 3151 6.035975 ACCTTTTTGAATCTTGCGAACTTTTG 59.964 34.615 0.00 0.00 0.00 2.44
2418 3160 4.797868 TCTTGCGAACTTTTGTTGAACATG 59.202 37.500 0.00 0.00 43.66 3.21
2485 3248 6.833416 CCCAACCTGTATTCTTTCATTATCCA 59.167 38.462 0.00 0.00 0.00 3.41
2519 3282 5.710099 GGGATTCCGGCTATTGAAATGATTA 59.290 40.000 0.00 0.00 0.00 1.75
2553 3316 7.649533 AAGCATCATTTTGGTATCATCTTGA 57.350 32.000 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
140 172 1.600916 GCCGTGAAGAAAGGGCTGT 60.601 57.895 0.83 0.00 45.59 4.40
147 179 2.358247 GAGCCGGCCGTGAAGAAA 60.358 61.111 26.15 0.00 0.00 2.52
312 365 4.315588 GCTGTCAGGAGCTGCAAT 57.684 55.556 8.35 0.00 35.95 3.56
336 392 2.521103 CCGTCCTCATGGGAGTCAT 58.479 57.895 0.00 0.00 46.10 3.06
337 393 4.034246 CCGTCCTCATGGGAGTCA 57.966 61.111 0.00 0.00 46.10 3.41
374 430 3.258228 AATCTGCTGCCAGCGACCA 62.258 57.895 12.80 0.00 46.26 4.02
521 600 4.266714 ACCTTCGTTACAAATACCCATGG 58.733 43.478 4.14 4.14 0.00 3.66
522 601 5.526111 CCTACCTTCGTTACAAATACCCATG 59.474 44.000 0.00 0.00 0.00 3.66
523 602 5.426185 TCCTACCTTCGTTACAAATACCCAT 59.574 40.000 0.00 0.00 0.00 4.00
524 603 4.776837 TCCTACCTTCGTTACAAATACCCA 59.223 41.667 0.00 0.00 0.00 4.51
605 1062 1.608025 GCAGGAAACACAGATCCGTCA 60.608 52.381 0.00 0.00 40.78 4.35
746 1245 0.042188 CGTGAAACCGTTCAGTGCAG 60.042 55.000 0.00 0.00 44.44 4.41
750 1249 2.877974 GCGCGTGAAACCGTTCAGT 61.878 57.895 8.43 0.00 44.44 3.41
797 1313 2.510874 CGGACGCGCAATTATTTTTCA 58.489 42.857 5.73 0.00 0.00 2.69
799 1315 1.264672 GCGGACGCGCAATTATTTTT 58.735 45.000 5.73 0.00 34.62 1.94
801 1317 4.682306 GCGGACGCGCAATTATTT 57.318 50.000 5.73 0.00 34.62 1.40
1491 2056 4.568359 CGGTCATCATCAGACGAAAAGATT 59.432 41.667 0.00 0.00 36.87 2.40
1558 2134 4.585879 TCATCATCATCATCATCGCCATT 58.414 39.130 0.00 0.00 0.00 3.16
1907 2601 3.843999 ACTGACGCTTTTTGCTCAAAAA 58.156 36.364 16.65 16.65 44.98 1.94
1911 2605 3.462982 TCTAACTGACGCTTTTTGCTCA 58.537 40.909 0.00 0.00 40.11 4.26
1963 2684 3.879295 CCATTTAGATACTGGTGCTGTGG 59.121 47.826 0.00 0.00 0.00 4.17
2044 2775 7.561021 AATTTGGTAAAAATGCGGAAAGTTT 57.439 28.000 0.00 0.00 0.00 2.66
2137 2877 3.013921 ACTGGAAGAGTTCACGCAAAAA 58.986 40.909 0.00 0.00 37.43 1.94
2138 2878 2.354510 CACTGGAAGAGTTCACGCAAAA 59.645 45.455 0.00 0.00 37.43 2.44
2139 2879 1.939934 CACTGGAAGAGTTCACGCAAA 59.060 47.619 0.00 0.00 37.43 3.68
2142 2882 2.086054 ATCACTGGAAGAGTTCACGC 57.914 50.000 0.00 0.00 37.43 5.34
2143 2883 6.727824 AAATAATCACTGGAAGAGTTCACG 57.272 37.500 0.00 0.00 37.43 4.35
2175 2915 9.868277 AACTCACAAATTTAAGAAATGTTCACA 57.132 25.926 0.00 0.00 0.00 3.58
2291 3033 9.937175 TTGAAAAGTTCAAAAACACGAAAAATT 57.063 22.222 0.99 0.00 45.94 1.82
2374 3116 9.650371 GCAAGATTCAAAAAGGTTAAAACATTC 57.350 29.630 0.00 0.00 30.85 2.67
2376 3118 7.708752 TCGCAAGATTCAAAAAGGTTAAAACAT 59.291 29.630 0.00 0.00 45.01 2.71
2377 3119 7.036220 TCGCAAGATTCAAAAAGGTTAAAACA 58.964 30.769 0.00 0.00 45.01 2.83
2378 3120 7.458038 TCGCAAGATTCAAAAAGGTTAAAAC 57.542 32.000 0.00 0.00 45.01 2.43
2401 3143 6.407475 AGCAAACATGTTCAACAAAAGTTC 57.593 33.333 12.39 0.00 0.00 3.01
2409 3151 9.463443 AAAATAAGAGTAGCAAACATGTTCAAC 57.537 29.630 12.39 7.85 0.00 3.18
2439 3181 6.427441 TGGGTCTTTGCCATACACAATAATA 58.573 36.000 0.00 0.00 0.00 0.98
2485 3248 4.184649 AGCCGGAATCCCTATGAAAAAT 57.815 40.909 5.05 0.00 0.00 1.82
2527 3290 9.187996 TCAAGATGATACCAAAATGATGCTTAA 57.812 29.630 0.00 0.00 0.00 1.85


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

AutoCloner maintained by Alex Coulton.