Multiple sequence alignment - TraesCS2A01G338000

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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 TraesCS2A01G338000 chr2A 100.000 4479 0 0 1 4479 572448255 572452733 0.000000e+00 8272.0
1 TraesCS2A01G338000 chr2A 99.183 734 6 0 1718 2451 758412286 758411553 0.000000e+00 1323.0
2 TraesCS2A01G338000 chr2A 89.894 188 13 4 4298 4479 735570844 735570657 2.080000e-58 237.0
3 TraesCS2A01G338000 chr5A 99.080 1740 16 0 2452 4191 554343627 554345366 0.000000e+00 3125.0
4 TraesCS2A01G338000 chr5A 99.130 1724 9 2 1 1718 554341911 554343634 0.000000e+00 3096.0
5 TraesCS2A01G338000 chr5A 97.954 733 15 0 1719 2451 29528911 29529643 0.000000e+00 1271.0
6 TraesCS2A01G338000 chr5A 89.094 1027 92 17 2549 3566 509219676 509220691 0.000000e+00 1258.0
7 TraesCS2A01G338000 chr5A 95.956 272 9 2 3602 3873 509220695 509220964 1.480000e-119 440.0
8 TraesCS2A01G338000 chr5A 87.838 222 26 1 529 750 492991449 492991229 4.440000e-65 259.0
9 TraesCS2A01G338000 chr5A 95.918 147 4 1 4335 4479 554345734 554345880 2.080000e-58 237.0
10 TraesCS2A01G338000 chr5A 86.385 213 27 2 261 472 492991448 492991237 9.690000e-57 231.0
11 TraesCS2A01G338000 chr5A 95.161 124 5 1 4188 4310 612924219 612924342 1.270000e-45 195.0
12 TraesCS2A01G338000 chr5D 92.792 1318 80 7 2549 3854 404873347 404872033 0.000000e+00 1893.0
13 TraesCS2A01G338000 chr5D 78.626 262 47 8 3445 3703 540083528 540083783 9.970000e-37 165.0
14 TraesCS2A01G338000 chr5B 90.030 1334 109 18 2551 3874 486039985 486038666 0.000000e+00 1705.0
15 TraesCS2A01G338000 chr5B 97.826 736 16 0 1716 2451 471135872 471136607 0.000000e+00 1271.0
16 TraesCS2A01G338000 chr5B 91.979 187 10 3 4298 4479 617661245 617661431 1.600000e-64 257.0
17 TraesCS2A01G338000 chr5B 90.909 187 12 3 4298 4479 396159736 396159922 3.460000e-61 246.0
18 TraesCS2A01G338000 chr5B 89.840 187 14 3 4298 4479 357130412 357130598 7.490000e-58 235.0
19 TraesCS2A01G338000 chr7B 99.183 734 6 0 1719 2452 215894018 215893285 0.000000e+00 1323.0
20 TraesCS2A01G338000 chr7B 97.538 731 18 0 1721 2451 446995307 446996037 0.000000e+00 1251.0
21 TraesCS2A01G338000 chr7B 85.577 624 81 7 1020 1635 179778865 179778243 0.000000e+00 645.0
22 TraesCS2A01G338000 chr7B 83.046 696 109 4 998 1684 179750603 179751298 1.370000e-174 623.0
23 TraesCS2A01G338000 chr7B 85.385 520 48 12 472 966 319047526 319047010 8.590000e-142 514.0
24 TraesCS2A01G338000 chr7B 89.085 284 29 2 472 755 408372556 408372837 7.130000e-93 351.0
25 TraesCS2A01G338000 chr7B 92.453 212 14 2 261 471 408372613 408372823 7.280000e-78 302.0
26 TraesCS2A01G338000 chr7B 91.080 213 16 3 261 472 319047469 319047259 7.330000e-73 285.0
27 TraesCS2A01G338000 chr7B 93.258 178 11 1 40 217 319047914 319047738 1.240000e-65 261.0
28 TraesCS2A01G338000 chr7B 90.374 187 17 1 31 217 408372159 408372344 1.240000e-60 244.0
29 TraesCS2A01G338000 chr7B 89.840 187 14 3 4298 4479 279843670 279843856 7.490000e-58 235.0
30 TraesCS2A01G338000 chr7B 89.305 187 15 3 4298 4479 49088470 49088656 3.480000e-56 230.0
31 TraesCS2A01G338000 chr1B 98.103 738 12 2 1715 2451 423958579 423959315 0.000000e+00 1284.0
32 TraesCS2A01G338000 chr1B 95.868 121 3 2 4188 4307 194367661 194367780 1.270000e-45 195.0
33 TraesCS2A01G338000 chr3A 98.093 734 14 0 1718 2451 364123113 364122380 0.000000e+00 1279.0
34 TraesCS2A01G338000 chr3A 88.288 222 25 1 529 750 661661044 661660824 9.550000e-67 265.0
35 TraesCS2A01G338000 chr3A 77.282 471 84 13 3226 3682 54880692 54880231 5.750000e-64 255.0
36 TraesCS2A01G338000 chr3A 87.793 213 24 2 261 472 661661043 661660832 9.620000e-62 248.0
37 TraesCS2A01G338000 chr6B 97.817 733 16 0 1719 2451 547650117 547649385 0.000000e+00 1266.0
38 TraesCS2A01G338000 chr6B 88.288 222 25 1 529 750 142692673 142692893 9.550000e-67 265.0
39 TraesCS2A01G338000 chr6B 87.793 213 24 2 261 472 142692674 142692885 9.620000e-62 248.0
40 TraesCS2A01G338000 chr6B 90.196 102 9 1 866 966 560981690 560981791 1.010000e-26 132.0
41 TraesCS2A01G338000 chr6B 79.439 107 16 3 866 966 560978452 560978346 2.240000e-08 71.3
42 TraesCS2A01G338000 chr3B 97.548 734 16 2 1719 2451 638979126 638979858 0.000000e+00 1254.0
43 TraesCS2A01G338000 chr3B 78.761 452 76 13 3245 3682 66800286 66799841 7.330000e-73 285.0
44 TraesCS2A01G338000 chr7D 86.747 664 81 5 1020 1676 219888776 219889439 0.000000e+00 732.0
45 TraesCS2A01G338000 chr7A 85.587 673 89 4 1020 1684 232459509 232458837 0.000000e+00 699.0
46 TraesCS2A01G338000 chr7A 88.288 222 25 1 529 750 561608174 561608394 9.550000e-67 265.0
47 TraesCS2A01G338000 chr7A 87.793 213 24 2 261 472 561608175 561608386 9.620000e-62 248.0
48 TraesCS2A01G338000 chr7A 89.840 187 14 3 4298 4479 343949140 343948954 7.490000e-58 235.0
49 TraesCS2A01G338000 chr7A 88.889 189 14 5 4298 4479 191270312 191270124 4.510000e-55 226.0
50 TraesCS2A01G338000 chr7A 95.868 121 4 1 4188 4307 11727434 11727554 1.270000e-45 195.0
51 TraesCS2A01G338000 chr7A 86.471 170 18 5 3467 3634 24465688 24465854 9.900000e-42 182.0
52 TraesCS2A01G338000 chr4B 84.794 388 33 11 604 966 496440798 496441184 2.550000e-97 366.0
53 TraesCS2A01G338000 chr4B 90.909 187 16 1 31 217 496429860 496430045 2.680000e-62 250.0
54 TraesCS2A01G338000 chr4B 97.458 118 2 1 4188 4305 642779808 642779692 2.730000e-47 200.0
55 TraesCS2A01G338000 chr4B 95.833 120 5 0 4188 4307 144406297 144406178 1.270000e-45 195.0
56 TraesCS2A01G338000 chr4B 90.647 139 12 1 334 472 496440798 496440935 2.750000e-42 183.0
57 TraesCS2A01G338000 chr1D 86.527 334 32 6 3870 4191 201924892 201924560 5.510000e-94 355.0
58 TraesCS2A01G338000 chr6A 88.341 223 24 2 529 750 495440732 495440511 2.660000e-67 267.0
59 TraesCS2A01G338000 chr6A 87.324 213 26 1 261 472 495440731 495440519 4.480000e-60 243.0
60 TraesCS2A01G338000 chr6A 95.902 122 3 1 4188 4307 523555979 523556100 3.530000e-46 196.0
61 TraesCS2A01G338000 chr2B 90.909 187 16 1 31 217 639452786 639452971 2.680000e-62 250.0
62 TraesCS2A01G338000 chr2B 90.960 177 15 1 41 217 639438237 639438412 2.080000e-58 237.0
63 TraesCS2A01G338000 chr2B 90.960 177 15 1 41 217 639439018 639439193 2.080000e-58 237.0
64 TraesCS2A01G338000 chr2B 94.156 154 7 2 64 217 639432071 639432222 2.690000e-57 233.0
65 TraesCS2A01G338000 chr2B 88.770 187 18 3 31 217 639425724 639425907 4.510000e-55 226.0
66 TraesCS2A01G338000 chr2D 95.868 121 4 1 4188 4308 282923556 282923675 1.270000e-45 195.0
67 TraesCS2A01G338000 chr1A 91.971 137 5 5 4188 4320 276418839 276418973 2.130000e-43 187.0
68 TraesCS2A01G338000 chr1A 94.565 92 5 0 2452 2543 352130581 352130490 4.670000e-30 143.0
69 TraesCS2A01G338000 chr1A 94.565 92 4 1 2452 2543 7306443 7306533 1.680000e-29 141.0
70 TraesCS2A01G338000 chr4A 94.872 117 4 2 4188 4304 94143683 94143797 9.900000e-42 182.0
71 TraesCS2A01G338000 chr3D 89.412 85 7 2 883 966 584117615 584117698 6.130000e-19 106.0


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 TraesCS2A01G338000 chr2A 572448255 572452733 4478 False 8272.000000 8272 100.000000 1 4479 1 chr2A.!!$F1 4478
1 TraesCS2A01G338000 chr2A 758411553 758412286 733 True 1323.000000 1323 99.183000 1718 2451 1 chr2A.!!$R2 733
2 TraesCS2A01G338000 chr5A 554341911 554345880 3969 False 2152.666667 3125 98.042667 1 4479 3 chr5A.!!$F4 4478
3 TraesCS2A01G338000 chr5A 29528911 29529643 732 False 1271.000000 1271 97.954000 1719 2451 1 chr5A.!!$F1 732
4 TraesCS2A01G338000 chr5A 509219676 509220964 1288 False 849.000000 1258 92.525000 2549 3873 2 chr5A.!!$F3 1324
5 TraesCS2A01G338000 chr5D 404872033 404873347 1314 True 1893.000000 1893 92.792000 2549 3854 1 chr5D.!!$R1 1305
6 TraesCS2A01G338000 chr5B 486038666 486039985 1319 True 1705.000000 1705 90.030000 2551 3874 1 chr5B.!!$R1 1323
7 TraesCS2A01G338000 chr5B 471135872 471136607 735 False 1271.000000 1271 97.826000 1716 2451 1 chr5B.!!$F3 735
8 TraesCS2A01G338000 chr7B 215893285 215894018 733 True 1323.000000 1323 99.183000 1719 2452 1 chr7B.!!$R2 733
9 TraesCS2A01G338000 chr7B 446995307 446996037 730 False 1251.000000 1251 97.538000 1721 2451 1 chr7B.!!$F4 730
10 TraesCS2A01G338000 chr7B 179778243 179778865 622 True 645.000000 645 85.577000 1020 1635 1 chr7B.!!$R1 615
11 TraesCS2A01G338000 chr7B 179750603 179751298 695 False 623.000000 623 83.046000 998 1684 1 chr7B.!!$F2 686
12 TraesCS2A01G338000 chr7B 319047010 319047914 904 True 353.333333 514 89.907667 40 966 3 chr7B.!!$R3 926
13 TraesCS2A01G338000 chr7B 408372159 408372837 678 False 299.000000 351 90.637333 31 755 3 chr7B.!!$F5 724
14 TraesCS2A01G338000 chr1B 423958579 423959315 736 False 1284.000000 1284 98.103000 1715 2451 1 chr1B.!!$F2 736
15 TraesCS2A01G338000 chr3A 364122380 364123113 733 True 1279.000000 1279 98.093000 1718 2451 1 chr3A.!!$R2 733
16 TraesCS2A01G338000 chr6B 547649385 547650117 732 True 1266.000000 1266 97.817000 1719 2451 1 chr6B.!!$R1 732
17 TraesCS2A01G338000 chr3B 638979126 638979858 732 False 1254.000000 1254 97.548000 1719 2451 1 chr3B.!!$F1 732
18 TraesCS2A01G338000 chr7D 219888776 219889439 663 False 732.000000 732 86.747000 1020 1676 1 chr7D.!!$F1 656
19 TraesCS2A01G338000 chr7A 232458837 232459509 672 True 699.000000 699 85.587000 1020 1684 1 chr7A.!!$R2 664
20 TraesCS2A01G338000 chr2B 639438237 639439193 956 False 237.000000 237 90.960000 41 217 2 chr2B.!!$F4 176

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
203 204 0.179111 TCGAGTGGCGGATCAACATC 60.179 55.000 0.00 0.0 41.33 3.06 F
225 226 3.749632 CGGAAGGAACCCAAACTAACCTT 60.750 47.826 0.00 0.0 39.89 3.50 F
585 665 6.073980 GCAGTTTTGTCAATACACTTCGTCTA 60.074 38.462 8.59 0.0 34.61 2.59 F
2043 2427 6.530120 AGATATGGTCAACACACAACAAGTA 58.470 36.000 0.00 0.0 0.00 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2057 2441 0.756294 TGAGCTTTTCAGTCGTGGGA 59.244 50.000 0.00 0.0 0.00 4.37 R
2452 2865 5.414454 GGATAAGCACTTGGTGTTGTTATCA 59.586 40.000 18.94 0.0 36.18 2.15 R
2457 2870 3.149196 CAGGATAAGCACTTGGTGTTGT 58.851 45.455 0.00 0.0 35.75 3.32 R
4197 4629 0.330604 AACTCATGGCTCTGGCACAT 59.669 50.000 0.00 0.0 41.84 3.21 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
203 204 0.179111 TCGAGTGGCGGATCAACATC 60.179 55.000 0.00 0.00 41.33 3.06
225 226 3.749632 CGGAAGGAACCCAAACTAACCTT 60.750 47.826 0.00 0.00 39.89 3.50
585 665 6.073980 GCAGTTTTGTCAATACACTTCGTCTA 60.074 38.462 8.59 0.00 34.61 2.59
2043 2427 6.530120 AGATATGGTCAACACACAACAAGTA 58.470 36.000 0.00 0.00 0.00 2.24
2057 2441 7.754924 CACACAACAAGTATCAAAAAGACAACT 59.245 33.333 0.00 0.00 0.00 3.16
2454 2867 9.548631 TTTAATAACCATTCCCAGGTTTAATGA 57.451 29.630 2.64 0.00 46.85 2.57
2455 2868 9.722317 TTAATAACCATTCCCAGGTTTAATGAT 57.278 29.630 2.64 0.00 46.85 2.45
2457 2870 9.722317 AATAACCATTCCCAGGTTTAATGATAA 57.278 29.630 2.64 0.00 46.85 1.75
2895 3314 8.970020 TCATAAGCATCCATGTGTCTTATTTTT 58.030 29.630 0.00 0.00 31.87 1.94
3577 4000 6.151985 TGTTTCTTTTGGTGTATGTGAAGTGT 59.848 34.615 0.00 0.00 0.00 3.55
3744 4176 5.471456 CAGAGGTTATTGCTGTCCATATTCC 59.529 44.000 0.00 0.00 0.00 3.01
3797 4229 6.883744 TGTTATCCATGTATCACACAAGCTA 58.116 36.000 0.00 0.00 41.55 3.32
3926 4358 8.274322 TGGATCAATATTCTGGACATTACAAGT 58.726 33.333 0.00 0.00 0.00 3.16
4047 4479 2.604686 AGAAGCGAGGCCTGGACA 60.605 61.111 20.35 0.00 0.00 4.02
4065 4497 0.035317 CAACAGGTGGTAGAGCAGCA 59.965 55.000 12.86 0.00 0.00 4.41
4191 4623 7.212976 TGGAGAATCTTATGTATGTCTCTTGC 58.787 38.462 0.00 0.00 33.56 4.01
4192 4624 7.070447 TGGAGAATCTTATGTATGTCTCTTGCT 59.930 37.037 0.00 0.00 33.56 3.91
4196 4628 9.364989 GAATCTTATGTATGTCTCTTGCTATCC 57.635 37.037 0.00 0.00 0.00 2.59
4197 4629 7.839680 TCTTATGTATGTCTCTTGCTATCCA 57.160 36.000 0.00 0.00 0.00 3.41
4200 4632 5.876651 TGTATGTCTCTTGCTATCCATGT 57.123 39.130 0.00 0.00 0.00 3.21
4201 4633 5.604565 TGTATGTCTCTTGCTATCCATGTG 58.395 41.667 0.00 0.00 0.00 3.21
4202 4634 2.910199 TGTCTCTTGCTATCCATGTGC 58.090 47.619 0.00 0.00 0.00 4.57
4203 4635 2.216898 GTCTCTTGCTATCCATGTGCC 58.783 52.381 0.00 0.00 0.00 5.01
4204 4636 1.839354 TCTCTTGCTATCCATGTGCCA 59.161 47.619 0.00 0.00 0.00 4.92
4208 4640 0.179037 TGCTATCCATGTGCCAGAGC 60.179 55.000 0.00 0.00 40.48 4.09
4209 4641 0.888285 GCTATCCATGTGCCAGAGCC 60.888 60.000 0.00 0.00 38.69 4.70
4212 4644 0.467474 ATCCATGTGCCAGAGCCATG 60.467 55.000 8.59 8.59 42.54 3.66
4213 4645 1.077285 CCATGTGCCAGAGCCATGA 60.077 57.895 14.22 0.00 44.14 3.07
4214 4646 1.101635 CCATGTGCCAGAGCCATGAG 61.102 60.000 14.22 5.17 44.14 2.90
4215 4647 0.393944 CATGTGCCAGAGCCATGAGT 60.394 55.000 0.00 0.00 44.14 3.41
4216 4648 0.330604 ATGTGCCAGAGCCATGAGTT 59.669 50.000 0.00 0.00 38.69 3.01
4217 4649 0.607217 TGTGCCAGAGCCATGAGTTG 60.607 55.000 0.00 0.00 38.69 3.16
4226 4658 3.231734 CCATGAGTTGGTTGCGAGA 57.768 52.632 0.00 0.00 40.99 4.04
4228 4660 1.667724 CCATGAGTTGGTTGCGAGATC 59.332 52.381 0.00 0.00 40.99 2.75
4229 4661 2.625737 CATGAGTTGGTTGCGAGATCT 58.374 47.619 0.00 0.00 0.00 2.75
4230 4662 2.839486 TGAGTTGGTTGCGAGATCTT 57.161 45.000 0.00 0.00 0.00 2.40
4231 4663 3.953712 TGAGTTGGTTGCGAGATCTTA 57.046 42.857 0.00 0.00 0.00 2.10
4233 4665 4.183865 TGAGTTGGTTGCGAGATCTTATG 58.816 43.478 0.00 0.00 0.00 1.90
4234 4666 3.535561 AGTTGGTTGCGAGATCTTATGG 58.464 45.455 0.00 0.00 0.00 2.74
4235 4667 2.614057 GTTGGTTGCGAGATCTTATGGG 59.386 50.000 0.00 0.00 0.00 4.00
4236 4668 1.837439 TGGTTGCGAGATCTTATGGGT 59.163 47.619 0.00 0.00 0.00 4.51
4237 4669 2.238646 TGGTTGCGAGATCTTATGGGTT 59.761 45.455 0.00 0.00 0.00 4.11
4239 4671 3.312697 GGTTGCGAGATCTTATGGGTTTC 59.687 47.826 0.00 0.00 0.00 2.78
4240 4672 3.904800 TGCGAGATCTTATGGGTTTCA 57.095 42.857 0.00 0.00 0.00 2.69
4241 4673 3.531538 TGCGAGATCTTATGGGTTTCAC 58.468 45.455 0.00 0.00 0.00 3.18
4243 4675 3.432326 GCGAGATCTTATGGGTTTCACCT 60.432 47.826 0.00 0.00 38.64 4.00
4244 4676 4.770795 CGAGATCTTATGGGTTTCACCTT 58.229 43.478 0.00 0.00 38.64 3.50
4247 4679 6.480320 CGAGATCTTATGGGTTTCACCTTTAG 59.520 42.308 0.00 0.00 38.64 1.85
4248 4680 6.122964 AGATCTTATGGGTTTCACCTTTAGC 58.877 40.000 0.00 0.00 38.64 3.09
4252 4684 3.428413 TGGGTTTCACCTTTAGCCTAC 57.572 47.619 0.00 0.00 38.64 3.18
4254 4686 2.619849 GGGTTTCACCTTTAGCCTACCC 60.620 54.545 0.00 0.00 38.64 3.69
4255 4687 2.619849 GGTTTCACCTTTAGCCTACCCC 60.620 54.545 0.00 0.00 34.73 4.95
4257 4689 2.047769 TCACCTTTAGCCTACCCCAA 57.952 50.000 0.00 0.00 0.00 4.12
4258 4690 1.631898 TCACCTTTAGCCTACCCCAAC 59.368 52.381 0.00 0.00 0.00 3.77
4259 4691 1.633945 CACCTTTAGCCTACCCCAACT 59.366 52.381 0.00 0.00 0.00 3.16
4260 4692 2.041216 CACCTTTAGCCTACCCCAACTT 59.959 50.000 0.00 0.00 0.00 2.66
4261 4693 2.041216 ACCTTTAGCCTACCCCAACTTG 59.959 50.000 0.00 0.00 0.00 3.16
4264 4696 3.887916 TTAGCCTACCCCAACTTGTTT 57.112 42.857 0.00 0.00 0.00 2.83
4265 4697 1.995376 AGCCTACCCCAACTTGTTTG 58.005 50.000 0.00 0.00 34.63 2.93
4277 4709 5.262588 CAACTTGTTTGGAACTAAAGGCT 57.737 39.130 0.00 0.00 0.00 4.58
4278 4710 5.660460 CAACTTGTTTGGAACTAAAGGCTT 58.340 37.500 0.00 0.00 0.00 4.35
4279 4711 5.932619 ACTTGTTTGGAACTAAAGGCTTT 57.067 34.783 17.76 17.76 0.00 3.51
4281 4713 5.186992 ACTTGTTTGGAACTAAAGGCTTTGT 59.813 36.000 22.32 14.58 0.00 2.83
4283 4715 5.415221 TGTTTGGAACTAAAGGCTTTGTTG 58.585 37.500 22.32 13.85 0.00 3.33
4285 4717 5.669164 TTGGAACTAAAGGCTTTGTTGTT 57.331 34.783 22.32 20.82 0.00 2.83
4287 4719 4.464597 TGGAACTAAAGGCTTTGTTGTTGT 59.535 37.500 22.32 8.35 0.00 3.32
4290 4722 6.183360 GGAACTAAAGGCTTTGTTGTTGTTTG 60.183 38.462 22.32 0.00 0.00 2.93
4291 4723 5.789521 ACTAAAGGCTTTGTTGTTGTTTGT 58.210 33.333 22.32 0.00 0.00 2.83
4292 4724 6.227522 ACTAAAGGCTTTGTTGTTGTTTGTT 58.772 32.000 22.32 0.00 0.00 2.83
4293 4725 5.355467 AAAGGCTTTGTTGTTGTTTGTTG 57.645 34.783 12.53 0.00 0.00 3.33
4294 4726 4.001618 AGGCTTTGTTGTTGTTTGTTGT 57.998 36.364 0.00 0.00 0.00 3.32
4295 4727 4.384940 AGGCTTTGTTGTTGTTTGTTGTT 58.615 34.783 0.00 0.00 0.00 2.83
4296 4728 4.213059 AGGCTTTGTTGTTGTTTGTTGTTG 59.787 37.500 0.00 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 2.359376 TTCTTCCTCCATCCCCTTCA 57.641 50.000 0.00 0.00 0.00 3.02
203 204 2.156917 GGTTAGTTTGGGTTCCTTCCG 58.843 52.381 0.00 0.00 0.00 4.30
225 226 7.040062 AGGACAAATATGAAATCACCGTTGAAA 60.040 33.333 0.00 0.00 34.61 2.69
2043 2427 3.564225 GTCGTGGGAGTTGTCTTTTTGAT 59.436 43.478 0.00 0.00 0.00 2.57
2057 2441 0.756294 TGAGCTTTTCAGTCGTGGGA 59.244 50.000 0.00 0.00 0.00 4.37
2452 2865 5.414454 GGATAAGCACTTGGTGTTGTTATCA 59.586 40.000 18.94 0.00 36.18 2.15
2453 2866 5.648092 AGGATAAGCACTTGGTGTTGTTATC 59.352 40.000 14.15 14.15 35.14 1.75
2454 2867 5.415701 CAGGATAAGCACTTGGTGTTGTTAT 59.584 40.000 0.00 2.03 35.75 1.89
2455 2868 4.759693 CAGGATAAGCACTTGGTGTTGTTA 59.240 41.667 0.00 0.00 35.75 2.41
2456 2869 3.569701 CAGGATAAGCACTTGGTGTTGTT 59.430 43.478 0.00 0.00 35.75 2.83
2457 2870 3.149196 CAGGATAAGCACTTGGTGTTGT 58.851 45.455 0.00 0.00 35.75 3.32
2895 3314 5.644636 ACGAAAAGTTTGTAACCTGACTGAA 59.355 36.000 0.00 0.00 0.00 3.02
3577 4000 6.162777 GGCAGCAATGGAAATAAAGTTGTAA 58.837 36.000 0.00 0.00 0.00 2.41
3744 4176 9.754382 AACCTGAAAATAAAAGCATATGCATAG 57.246 29.630 28.62 8.98 45.16 2.23
4047 4479 0.987294 ATGCTGCTCTACCACCTGTT 59.013 50.000 0.00 0.00 0.00 3.16
4065 4497 3.710209 ACTTGTGCTTCTCTTAGGCAT 57.290 42.857 0.00 0.00 38.27 4.40
4191 4623 0.471191 TGGCTCTGGCACATGGATAG 59.529 55.000 0.00 0.00 38.20 2.08
4192 4624 1.142936 ATGGCTCTGGCACATGGATA 58.857 50.000 0.00 0.00 41.84 2.59
4195 4627 1.077285 TCATGGCTCTGGCACATGG 60.077 57.895 13.76 0.00 41.84 3.66
4196 4628 0.393944 ACTCATGGCTCTGGCACATG 60.394 55.000 8.97 8.97 41.84 3.21
4197 4629 0.330604 AACTCATGGCTCTGGCACAT 59.669 50.000 0.00 0.00 41.84 3.21
4200 4632 1.001764 CCAACTCATGGCTCTGGCA 60.002 57.895 0.00 0.00 43.80 4.92
4201 4633 3.915575 CCAACTCATGGCTCTGGC 58.084 61.111 0.00 0.00 43.80 4.85
4209 4641 2.625737 AGATCTCGCAACCAACTCATG 58.374 47.619 0.00 0.00 0.00 3.07
4212 4644 3.557595 CCATAAGATCTCGCAACCAACTC 59.442 47.826 0.00 0.00 0.00 3.01
4213 4645 3.535561 CCATAAGATCTCGCAACCAACT 58.464 45.455 0.00 0.00 0.00 3.16
4214 4646 2.614057 CCCATAAGATCTCGCAACCAAC 59.386 50.000 0.00 0.00 0.00 3.77
4215 4647 2.238646 ACCCATAAGATCTCGCAACCAA 59.761 45.455 0.00 0.00 0.00 3.67
4216 4648 1.837439 ACCCATAAGATCTCGCAACCA 59.163 47.619 0.00 0.00 0.00 3.67
4217 4649 2.622064 ACCCATAAGATCTCGCAACC 57.378 50.000 0.00 0.00 0.00 3.77
4218 4650 3.938963 TGAAACCCATAAGATCTCGCAAC 59.061 43.478 0.00 0.00 0.00 4.17
4235 4667 2.040679 TGGGGTAGGCTAAAGGTGAAAC 59.959 50.000 0.00 0.00 0.00 2.78
4236 4668 2.350419 TGGGGTAGGCTAAAGGTGAAA 58.650 47.619 0.00 0.00 0.00 2.69
4237 4669 2.040679 GTTGGGGTAGGCTAAAGGTGAA 59.959 50.000 0.00 0.00 0.00 3.18
4239 4671 1.633945 AGTTGGGGTAGGCTAAAGGTG 59.366 52.381 0.00 0.00 0.00 4.00
4240 4672 2.041216 CAAGTTGGGGTAGGCTAAAGGT 59.959 50.000 0.00 0.00 0.00 3.50
4241 4673 2.041216 ACAAGTTGGGGTAGGCTAAAGG 59.959 50.000 7.96 0.00 0.00 3.11
4243 4675 3.887916 AACAAGTTGGGGTAGGCTAAA 57.112 42.857 7.96 0.00 0.00 1.85
4244 4676 3.492337 CAAACAAGTTGGGGTAGGCTAA 58.508 45.455 7.96 0.00 33.18 3.09
4255 4687 5.262588 AGCCTTTAGTTCCAAACAAGTTG 57.737 39.130 0.00 0.00 36.94 3.16
4257 4689 5.186992 ACAAAGCCTTTAGTTCCAAACAAGT 59.813 36.000 0.00 0.00 0.00 3.16
4258 4690 5.660460 ACAAAGCCTTTAGTTCCAAACAAG 58.340 37.500 0.00 0.00 0.00 3.16
4259 4691 5.669164 ACAAAGCCTTTAGTTCCAAACAA 57.331 34.783 0.00 0.00 0.00 2.83
4260 4692 5.046950 ACAACAAAGCCTTTAGTTCCAAACA 60.047 36.000 0.00 0.00 0.00 2.83
4261 4693 5.416083 ACAACAAAGCCTTTAGTTCCAAAC 58.584 37.500 0.00 0.00 0.00 2.93
4264 4696 4.464597 ACAACAACAAAGCCTTTAGTTCCA 59.535 37.500 0.00 0.00 0.00 3.53
4265 4697 5.006153 ACAACAACAAAGCCTTTAGTTCC 57.994 39.130 0.00 0.00 0.00 3.62
4266 4698 6.367695 ACAAACAACAACAAAGCCTTTAGTTC 59.632 34.615 0.00 0.00 0.00 3.01
4268 4700 5.789521 ACAAACAACAACAAAGCCTTTAGT 58.210 33.333 0.00 0.00 0.00 2.24
4271 4703 4.819088 ACAACAAACAACAACAAAGCCTTT 59.181 33.333 0.00 0.00 0.00 3.11
4272 4704 4.384940 ACAACAAACAACAACAAAGCCTT 58.615 34.783 0.00 0.00 0.00 4.35
4273 4705 4.001618 ACAACAAACAACAACAAAGCCT 57.998 36.364 0.00 0.00 0.00 4.58
4275 4707 5.335827 TCAACAACAAACAACAACAAAGC 57.664 34.783 0.00 0.00 0.00 3.51
4276 4708 7.114882 TCATCAACAACAAACAACAACAAAG 57.885 32.000 0.00 0.00 0.00 2.77
4277 4709 7.482654 TTCATCAACAACAAACAACAACAAA 57.517 28.000 0.00 0.00 0.00 2.83
4278 4710 7.664082 ATTCATCAACAACAAACAACAACAA 57.336 28.000 0.00 0.00 0.00 2.83
4279 4711 7.664082 AATTCATCAACAACAAACAACAACA 57.336 28.000 0.00 0.00 0.00 3.33
4281 4713 7.536622 GCAAAATTCATCAACAACAAACAACAA 59.463 29.630 0.00 0.00 0.00 2.83
4283 4715 6.192500 CGCAAAATTCATCAACAACAAACAAC 59.808 34.615 0.00 0.00 0.00 3.32
4285 4717 5.578336 TCGCAAAATTCATCAACAACAAACA 59.422 32.000 0.00 0.00 0.00 2.83
4287 4719 6.647569 CATCGCAAAATTCATCAACAACAAA 58.352 32.000 0.00 0.00 0.00 2.83
4290 4722 4.150274 TGCATCGCAAAATTCATCAACAAC 59.850 37.500 0.00 0.00 34.76 3.32
4291 4723 4.304939 TGCATCGCAAAATTCATCAACAA 58.695 34.783 0.00 0.00 34.76 2.83
4292 4724 3.910648 TGCATCGCAAAATTCATCAACA 58.089 36.364 0.00 0.00 34.76 3.33
4293 4725 4.907188 TTGCATCGCAAAATTCATCAAC 57.093 36.364 0.00 0.00 45.96 3.18
4345 4984 4.323715 AATGAGTCCATATGTGCTGTCACA 60.324 41.667 1.24 7.23 43.71 3.58
4442 5100 2.844804 CGACCGAGAGTTTTATGACGAC 59.155 50.000 0.00 0.00 0.00 4.34


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

AutoCloner maintained by Alex Coulton.