Multiple sequence alignment - TraesCS2B01G273400

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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 TraesCS2B01G273400 chr2B 100.000 3136 0 0 1 3136 374684311 374687446 0.000000e+00 5792.0
1 TraesCS2B01G273400 chr2B 90.361 166 16 0 2393 2558 57102689 57102524 5.270000e-53 219.0
2 TraesCS2B01G273400 chr2B 91.579 95 7 1 298 391 93074158 93074252 2.540000e-26 130.0
3 TraesCS2B01G273400 chr2B 91.579 95 7 1 298 391 485445938 485446032 2.540000e-26 130.0
4 TraesCS2B01G273400 chr2B 88.889 81 5 3 397 476 178862895 178862818 2.570000e-16 97.1
5 TraesCS2B01G273400 chr2A 94.857 1614 39 13 773 2345 386056617 386058227 0.000000e+00 2481.0
6 TraesCS2B01G273400 chr2A 89.881 672 55 9 33 698 386008686 386009350 0.000000e+00 852.0
7 TraesCS2B01G273400 chr2A 79.913 229 39 7 83 306 703564873 703565099 9.000000e-36 161.0
8 TraesCS2B01G273400 chr2A 92.308 78 2 3 704 777 386011927 386012004 1.190000e-19 108.0
9 TraesCS2B01G273400 chr2A 88.764 89 6 4 693 777 386011376 386011464 4.280000e-19 106.0
10 TraesCS2B01G273400 chr2D 92.084 1579 77 18 1 1539 306489154 306490724 0.000000e+00 2180.0
11 TraesCS2B01G273400 chr2D 95.982 672 17 6 1728 2391 306493281 306493950 0.000000e+00 1083.0
12 TraesCS2B01G273400 chr2D 93.478 92 5 1 299 389 423119126 423119217 5.460000e-28 135.0
13 TraesCS2B01G273400 chr2D 92.553 94 6 1 298 390 298410363 298410270 1.960000e-27 134.0
14 TraesCS2B01G273400 chr2D 91.753 97 6 2 298 392 648567621 648567717 1.960000e-27 134.0
15 TraesCS2B01G273400 chr2D 92.537 67 3 2 396 461 69254219 69254284 9.260000e-16 95.3
16 TraesCS2B01G273400 chr4D 87.801 664 71 10 2393 3051 250768947 250768289 0.000000e+00 769.0
17 TraesCS2B01G273400 chr4D 97.727 88 2 0 3049 3136 328338678 328338765 5.420000e-33 152.0
18 TraesCS2B01G273400 chr4D 95.652 92 3 1 3046 3136 173996535 173996444 2.520000e-31 147.0
19 TraesCS2B01G273400 chr7D 93.385 514 30 2 2546 3056 183907701 183907189 0.000000e+00 758.0
20 TraesCS2B01G273400 chr7D 93.023 516 32 3 2553 3066 214679155 214679668 0.000000e+00 750.0
21 TraesCS2B01G273400 chr7D 90.361 166 16 0 2393 2558 404969511 404969676 5.270000e-53 219.0
22 TraesCS2B01G273400 chr7D 90.526 95 8 1 298 391 8596982 8596888 1.180000e-24 124.0
23 TraesCS2B01G273400 chr7D 89.691 97 8 2 298 392 430947009 430946913 4.250000e-24 122.0
24 TraesCS2B01G273400 chr7D 76.961 204 43 4 91 291 526531002 526530800 2.560000e-21 113.0
25 TraesCS2B01G273400 chr7D 90.000 70 5 2 396 464 73143550 73143482 4.310000e-14 89.8
26 TraesCS2B01G273400 chr7D 86.567 67 7 2 396 461 169350516 169350451 4.340000e-09 73.1
27 TraesCS2B01G273400 chr6D 93.439 503 32 1 2554 3056 55917967 55918468 0.000000e+00 745.0
28 TraesCS2B01G273400 chr6D 91.566 166 14 0 2393 2558 202839445 202839610 2.430000e-56 230.0
29 TraesCS2B01G273400 chr6D 91.667 96 5 3 298 392 121158478 121158385 2.540000e-26 130.0
30 TraesCS2B01G273400 chr6D 90.722 97 7 2 298 392 13074982 13075078 9.130000e-26 128.0
31 TraesCS2B01G273400 chr6D 90.323 93 8 1 298 389 37920305 37920397 1.530000e-23 121.0
32 TraesCS2B01G273400 chr6D 90.217 92 8 1 298 388 430021073 430020982 5.490000e-23 119.0
33 TraesCS2B01G273400 chr6D 88.000 100 10 2 297 394 14904693 14904792 1.980000e-22 117.0
34 TraesCS2B01G273400 chr6D 89.773 88 9 0 302 389 38883650 38883737 2.560000e-21 113.0
35 TraesCS2B01G273400 chr6D 88.421 95 9 2 298 391 460770951 460770858 2.560000e-21 113.0
36 TraesCS2B01G273400 chr6D 88.462 52 4 2 397 447 86735969 86736019 9.390000e-06 62.1
37 TraesCS2B01G273400 chr3B 89.744 585 51 4 2553 3136 778208117 778208693 0.000000e+00 739.0
38 TraesCS2B01G273400 chr3B 88.554 166 18 1 2393 2558 300136111 300135947 1.910000e-47 200.0
39 TraesCS2B01G273400 chr3B 76.891 238 47 6 74 306 11015677 11015443 9.130000e-26 128.0
40 TraesCS2B01G273400 chr3B 82.119 151 24 3 121 269 157380575 157380724 3.280000e-25 126.0
41 TraesCS2B01G273400 chr3B 77.500 200 39 6 74 269 593937502 593937699 7.110000e-22 115.0
42 TraesCS2B01G273400 chr3B 92.405 79 6 0 383 461 143311398 143311476 2.560000e-21 113.0
43 TraesCS2B01G273400 chr3B 91.176 68 4 2 396 462 708501291 708501357 1.200000e-14 91.6
44 TraesCS2B01G273400 chrUn 92.621 515 34 4 2553 3066 121706509 121705998 0.000000e+00 737.0
45 TraesCS2B01G273400 chrUn 92.039 515 36 3 2546 3057 44853621 44853109 0.000000e+00 719.0
46 TraesCS2B01G273400 chrUn 87.129 101 8 5 298 394 100088897 100088798 3.310000e-20 110.0
47 TraesCS2B01G273400 chrUn 84.884 86 13 0 305 390 160328318 160328403 1.550000e-13 87.9
48 TraesCS2B01G273400 chrUn 84.884 86 13 0 305 390 160390170 160390255 1.550000e-13 87.9
49 TraesCS2B01G273400 chrUn 84.884 86 13 0 305 390 245425483 245425568 1.550000e-13 87.9
50 TraesCS2B01G273400 chrUn 84.884 86 13 0 305 390 358292553 358292468 1.550000e-13 87.9
51 TraesCS2B01G273400 chrUn 84.884 86 13 0 305 390 383584179 383584264 1.550000e-13 87.9
52 TraesCS2B01G273400 chrUn 85.227 88 8 3 303 390 92749189 92749107 5.570000e-13 86.1
53 TraesCS2B01G273400 chrUn 94.118 51 2 1 342 392 48998618 48998569 3.350000e-10 76.8
54 TraesCS2B01G273400 chr6B 92.871 505 33 3 2553 3057 489822087 489822588 0.000000e+00 730.0
55 TraesCS2B01G273400 chr6B 90.426 94 8 1 298 390 14104705 14104798 4.250000e-24 122.0
56 TraesCS2B01G273400 chr6B 79.355 155 30 2 116 269 662251387 662251234 1.190000e-19 108.0
57 TraesCS2B01G273400 chr6B 79.646 113 20 3 191 303 43727676 43727785 9.330000e-11 78.7
58 TraesCS2B01G273400 chr1D 92.673 505 35 2 2553 3057 70466039 70466541 0.000000e+00 726.0
59 TraesCS2B01G273400 chr1D 89.583 96 8 2 298 391 416803207 416803112 1.530000e-23 121.0
60 TraesCS2B01G273400 chr1D 89.583 96 8 2 298 391 435361672 435361767 1.530000e-23 121.0
61 TraesCS2B01G273400 chr1D 78.646 192 32 7 116 304 80553402 80553217 5.490000e-23 119.0
62 TraesCS2B01G273400 chr1D 92.424 66 5 0 396 461 203264933 203264868 9.260000e-16 95.3
63 TraesCS2B01G273400 chr1D 80.435 92 18 0 121 212 229038542 229038633 1.560000e-08 71.3
64 TraesCS2B01G273400 chr1D 93.333 45 3 0 420 464 461204059 461204015 2.020000e-07 67.6
65 TraesCS2B01G273400 chr1B 90.361 166 15 1 2393 2558 311256176 311256340 1.890000e-52 217.0
66 TraesCS2B01G273400 chr1B 90.361 166 15 1 2393 2558 513689218 513689054 1.890000e-52 217.0
67 TraesCS2B01G273400 chr1B 97.727 88 2 0 3049 3136 235373005 235373092 5.420000e-33 152.0
68 TraesCS2B01G273400 chr1B 78.824 170 32 4 102 269 148434428 148434261 9.190000e-21 111.0
69 TraesCS2B01G273400 chr5B 89.759 166 17 0 2393 2558 231756601 231756436 2.450000e-51 213.0
70 TraesCS2B01G273400 chr5B 96.739 92 2 1 3046 3136 709520544 709520635 5.420000e-33 152.0
71 TraesCS2B01G273400 chr5B 90.909 44 3 1 259 302 706311441 706311483 1.210000e-04 58.4
72 TraesCS2B01G273400 chr3D 88.554 166 19 0 2393 2558 223717135 223716970 5.300000e-48 202.0
73 TraesCS2B01G273400 chr3D 91.667 96 6 2 298 392 401169768 401169674 7.060000e-27 132.0
74 TraesCS2B01G273400 chr3D 90.722 97 7 2 298 393 358634909 358634814 9.130000e-26 128.0
75 TraesCS2B01G273400 chr3D 75.909 220 42 7 73 284 402341667 402341883 5.530000e-18 102.0
76 TraesCS2B01G273400 chr3D 78.767 146 30 1 123 267 462248198 462248053 2.570000e-16 97.1
77 TraesCS2B01G273400 chr3D 91.045 67 4 2 396 461 8367989 8367924 4.310000e-14 89.8
78 TraesCS2B01G273400 chr3D 91.045 67 4 2 396 461 8396862 8396797 4.310000e-14 89.8
79 TraesCS2B01G273400 chr4B 96.739 92 2 1 3046 3136 607859285 607859194 5.420000e-33 152.0
80 TraesCS2B01G273400 chr4B 91.398 93 7 1 298 389 21211038 21210946 3.280000e-25 126.0
81 TraesCS2B01G273400 chr4B 90.625 96 8 1 297 391 408974851 408974946 3.280000e-25 126.0
82 TraesCS2B01G273400 chr4B 89.474 95 9 1 298 391 107458828 107458734 5.490000e-23 119.0
83 TraesCS2B01G273400 chr7B 94.792 96 4 1 3042 3136 292540466 292540371 7.010000e-32 148.0
84 TraesCS2B01G273400 chr7B 80.132 151 24 5 73 221 563674200 563674054 1.190000e-19 108.0
85 TraesCS2B01G273400 chr7B 91.304 69 4 2 396 463 13318456 13318389 3.330000e-15 93.5
86 TraesCS2B01G273400 chr7B 90.278 72 5 2 396 466 191891976 191891906 3.330000e-15 93.5
87 TraesCS2B01G273400 chr7B 75.238 210 42 9 102 305 3682316 3682521 1.200000e-14 91.6
88 TraesCS2B01G273400 chr7B 74.554 224 49 6 73 291 655569643 655569863 1.200000e-14 91.6
89 TraesCS2B01G273400 chr7B 89.655 58 4 2 396 452 127754107 127754163 4.340000e-09 73.1
90 TraesCS2B01G273400 chr5D 94.792 96 4 1 3042 3136 115281824 115281919 7.010000e-32 148.0
91 TraesCS2B01G273400 chr5D 90.426 94 8 1 298 390 396921557 396921650 4.250000e-24 122.0
92 TraesCS2B01G273400 chr5D 94.828 58 1 2 396 452 314438939 314438995 4.310000e-14 89.8
93 TraesCS2B01G273400 chr5D 94.737 57 3 0 396 452 350730590 350730534 4.310000e-14 89.8
94 TraesCS2B01G273400 chr7A 79.186 221 38 5 91 305 131938432 131938650 2.520000e-31 147.0
95 TraesCS2B01G273400 chr7A 93.814 97 5 1 3040 3136 679100899 679100994 9.060000e-31 145.0
96 TraesCS2B01G273400 chr3A 91.667 96 6 2 298 392 661788369 661788463 7.060000e-27 132.0
97 TraesCS2B01G273400 chr3A 76.355 203 43 4 90 290 61221994 61222193 1.540000e-18 104.0
98 TraesCS2B01G273400 chr1A 93.258 89 5 1 298 385 119041107 119041195 2.540000e-26 130.0
99 TraesCS2B01G273400 chr1A 91.045 67 4 2 396 461 151337539 151337474 4.310000e-14 89.8
100 TraesCS2B01G273400 chr4A 89.109 101 9 2 298 397 37069162 37069063 1.180000e-24 124.0
101 TraesCS2B01G273400 chr4A 79.851 134 24 3 159 291 477055524 477055655 9.260000e-16 95.3
102 TraesCS2B01G273400 chr6A 91.045 67 4 2 396 461 208152936 208152871 4.310000e-14 89.8
103 TraesCS2B01G273400 chr6A 92.727 55 2 2 396 449 2792206 2792259 9.330000e-11 78.7


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 TraesCS2B01G273400 chr2B 374684311 374687446 3135 False 5792.000000 5792 100.000000 1 3136 1 chr2B.!!$F2 3135
1 TraesCS2B01G273400 chr2A 386056617 386058227 1610 False 2481.000000 2481 94.857000 773 2345 1 chr2A.!!$F1 1572
2 TraesCS2B01G273400 chr2A 386008686 386012004 3318 False 355.333333 852 90.317667 33 777 3 chr2A.!!$F3 744
3 TraesCS2B01G273400 chr2D 306489154 306493950 4796 False 1631.500000 2180 94.033000 1 2391 2 chr2D.!!$F4 2390
4 TraesCS2B01G273400 chr4D 250768289 250768947 658 True 769.000000 769 87.801000 2393 3051 1 chr4D.!!$R2 658
5 TraesCS2B01G273400 chr7D 183907189 183907701 512 True 758.000000 758 93.385000 2546 3056 1 chr7D.!!$R4 510
6 TraesCS2B01G273400 chr7D 214679155 214679668 513 False 750.000000 750 93.023000 2553 3066 1 chr7D.!!$F1 513
7 TraesCS2B01G273400 chr6D 55917967 55918468 501 False 745.000000 745 93.439000 2554 3056 1 chr6D.!!$F5 502
8 TraesCS2B01G273400 chr3B 778208117 778208693 576 False 739.000000 739 89.744000 2553 3136 1 chr3B.!!$F5 583
9 TraesCS2B01G273400 chrUn 121705998 121706509 511 True 737.000000 737 92.621000 2553 3066 1 chrUn.!!$R5 513
10 TraesCS2B01G273400 chrUn 44853109 44853621 512 True 719.000000 719 92.039000 2546 3057 1 chrUn.!!$R1 511
11 TraesCS2B01G273400 chr6B 489822087 489822588 501 False 730.000000 730 92.871000 2553 3057 1 chr6B.!!$F3 504
12 TraesCS2B01G273400 chr1D 70466039 70466541 502 False 726.000000 726 92.673000 2553 3057 1 chr1D.!!$F1 504

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
170 175 0.108615 CCGAGAAACTGAGCCGACAT 60.109 55.0 0.0 0.0 0.0 3.06 F
1051 3651 0.322546 GCCTCCAACCGATCCAAACT 60.323 55.0 0.0 0.0 0.0 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1211 3829 0.538584 TGATCATCTTCGGCTGCACT 59.461 50.0 0.50 0.00 0.0 4.40 R
2542 7646 0.029567 CGACGAGACTAGTGGCCATC 59.970 60.0 9.72 1.23 0.0 3.51 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
61 62 1.640593 TTGGTGTCTGTGAGGGGCAA 61.641 55.000 0.00 0.00 0.00 4.52
89 90 3.106242 TGTGTACAGATGCAGACGTTT 57.894 42.857 0.00 0.00 0.00 3.60
106 107 7.437124 CAGACGTTTATACATATGCACATACG 58.563 38.462 1.58 10.16 0.00 3.06
141 146 1.464608 CGCACACACACCCTTATCTTG 59.535 52.381 0.00 0.00 0.00 3.02
149 154 4.225042 ACACACCCTTATCTTGTGAGCATA 59.775 41.667 7.90 0.00 42.77 3.14
170 175 0.108615 CCGAGAAACTGAGCCGACAT 60.109 55.000 0.00 0.00 0.00 3.06
264 269 2.181975 CATCACCCAAAGGCCTGAAAT 58.818 47.619 5.69 0.00 36.11 2.17
270 275 4.020307 CACCCAAAGGCCTGAAATAAATGT 60.020 41.667 5.69 0.00 36.11 2.71
271 276 4.020307 ACCCAAAGGCCTGAAATAAATGTG 60.020 41.667 5.69 0.00 36.11 3.21
273 278 4.222588 CCAAAGGCCTGAAATAAATGTGGA 59.777 41.667 5.69 0.00 0.00 4.02
274 279 5.279910 CCAAAGGCCTGAAATAAATGTGGAA 60.280 40.000 5.69 0.00 0.00 3.53
303 308 3.127721 CGAGCATCAGTGTCAAGTCTAGA 59.872 47.826 0.00 0.00 33.17 2.43
309 314 5.651387 TCAGTGTCAAGTCTAGAATCTGG 57.349 43.478 0.00 0.00 0.00 3.86
313 318 4.808364 GTGTCAAGTCTAGAATCTGGATGC 59.192 45.833 0.00 0.00 0.00 3.91
337 342 9.770097 TGCAATTTTTATTATTTCTGGTGTTCA 57.230 25.926 0.00 0.00 0.00 3.18
370 375 8.362639 TGTCATGATTGAAGATGAATAGATCGA 58.637 33.333 0.00 0.00 32.48 3.59
381 386 9.658799 AAGATGAATAGATCGAAAGTTTTCTCA 57.341 29.630 0.00 0.00 35.07 3.27
468 474 4.488126 CCACATGTTGGTTCACTTAGTG 57.512 45.455 5.94 5.94 41.10 2.74
493 499 7.070198 TGTCCCTTTTCTATGGTCGATACATTA 59.930 37.037 10.27 0.00 0.00 1.90
555 561 5.278758 CCATTTTGTTAGTTCCGTGGTCAAT 60.279 40.000 0.00 0.00 0.00 2.57
933 3521 5.180117 CAGTAGGAATTGTCAAGTGGTTCAG 59.820 44.000 0.00 0.00 0.00 3.02
940 3528 0.843309 TCAAGTGGTTCAGGGCTTGA 59.157 50.000 0.00 0.00 43.16 3.02
1030 3630 0.470833 CCACCAAATCCACCAACCCA 60.471 55.000 0.00 0.00 0.00 4.51
1051 3651 0.322546 GCCTCCAACCGATCCAAACT 60.323 55.000 0.00 0.00 0.00 2.66
1102 3702 2.223249 CGCAATCCGGTACCATTTCTTG 60.223 50.000 13.54 8.71 0.00 3.02
1104 3704 3.016736 CAATCCGGTACCATTTCTTGCT 58.983 45.455 13.54 0.00 0.00 3.91
1540 6629 6.299141 TCTTATCTTAGATGGTTGGGAATGC 58.701 40.000 4.78 0.00 0.00 3.56
1598 6687 6.035112 TGGTTTCGTAAAAACTGCATTTCAAC 59.965 34.615 0.00 0.00 33.01 3.18
1647 6744 2.459934 CGCTCCTTGGTGTTGAAAAAC 58.540 47.619 0.00 0.00 0.00 2.43
1649 6746 3.706698 GCTCCTTGGTGTTGAAAAACTC 58.293 45.455 0.00 0.00 0.00 3.01
1754 6851 4.829064 TTAATGATGCCTTTATCCGTGC 57.171 40.909 0.00 0.00 0.00 5.34
2024 7122 7.336427 CAGAAGCTTTTAAGATGTCAGGAGAAT 59.664 37.037 0.00 0.00 0.00 2.40
2081 7182 2.299326 AAGGAATGTCCAGCAGCTTT 57.701 45.000 0.00 0.00 39.61 3.51
2192 7293 0.976641 TTTGTGTGCAAACCACCCAA 59.023 45.000 4.11 0.00 44.01 4.12
2243 7347 1.074727 CAGTGGGTGACAATGGGGTAA 59.925 52.381 0.00 0.00 41.27 2.85
2351 7455 3.525800 ACCCCCATAGCACATATTTCC 57.474 47.619 0.00 0.00 0.00 3.13
2353 7457 3.467103 ACCCCCATAGCACATATTTCCTT 59.533 43.478 0.00 0.00 0.00 3.36
2391 7495 8.082334 TGGCATGAGCAAGTTTAAATTTTTAC 57.918 30.769 0.00 0.00 44.61 2.01
2417 7521 3.010420 GTTAGGCTCAATCAACCACCTC 58.990 50.000 0.00 0.00 0.00 3.85
2419 7523 2.551270 AGGCTCAATCAACCACCTCTA 58.449 47.619 0.00 0.00 0.00 2.43
2420 7524 2.503356 AGGCTCAATCAACCACCTCTAG 59.497 50.000 0.00 0.00 0.00 2.43
2430 7534 2.044555 CACCTCTAGTCGCGGGTCA 61.045 63.158 6.13 0.00 0.00 4.02
2450 7554 2.342648 GACACGGACGGGAGCTTT 59.657 61.111 0.00 0.00 0.00 3.51
2452 7556 3.423154 CACGGACGGGAGCTTTGC 61.423 66.667 0.00 0.00 0.00 3.68
2481 7585 1.544314 GCTGGTAGATCTTCATGCCCC 60.544 57.143 0.00 0.00 0.00 5.80
2497 7601 4.785453 CCCCTCAACCAGCTCGCC 62.785 72.222 0.00 0.00 0.00 5.54
2499 7603 3.710722 CCTCAACCAGCTCGCCCT 61.711 66.667 0.00 0.00 0.00 5.19
2501 7605 2.922503 TCAACCAGCTCGCCCTCA 60.923 61.111 0.00 0.00 0.00 3.86
2504 7608 3.245668 AACCAGCTCGCCCTCACTG 62.246 63.158 0.00 0.00 0.00 3.66
2513 7617 0.315568 CGCCCTCACTGTAGCTATCC 59.684 60.000 0.00 0.00 0.00 2.59
2515 7619 2.043227 GCCCTCACTGTAGCTATCCTT 58.957 52.381 0.00 0.00 0.00 3.36
2533 7637 3.729966 CCTTAGAAAAGGTATCCTCGCC 58.270 50.000 0.00 0.00 46.34 5.54
2538 7642 1.213296 AAAGGTATCCTCGCCACCAT 58.787 50.000 0.00 0.00 34.62 3.55
2539 7643 0.759346 AAGGTATCCTCGCCACCATC 59.241 55.000 0.00 0.00 34.62 3.51
2540 7644 0.398522 AGGTATCCTCGCCACCATCA 60.399 55.000 0.00 0.00 34.62 3.07
2541 7645 0.034059 GGTATCCTCGCCACCATCAG 59.966 60.000 0.00 0.00 32.32 2.90
2542 7646 0.034059 GTATCCTCGCCACCATCAGG 59.966 60.000 0.00 0.00 42.21 3.86
2543 7647 0.105709 TATCCTCGCCACCATCAGGA 60.106 55.000 0.00 0.00 39.42 3.86
2544 7648 0.765903 ATCCTCGCCACCATCAGGAT 60.766 55.000 0.00 0.00 40.38 3.24
2568 7672 1.995484 CACTAGTCTCGTCGGACGTAA 59.005 52.381 27.53 15.40 43.14 3.18
2645 7749 1.472662 CCAAGTCAGACGGGTCCACT 61.473 60.000 6.22 0.00 0.00 4.00
2722 7826 0.107643 GCATCAGCCTTCCTACCTCC 59.892 60.000 0.00 0.00 33.58 4.30
3105 8212 2.356695 AGTTACCACCACTTGCGTTTTC 59.643 45.455 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 1.459209 CGAAGCAGAACATACGCACAA 59.541 47.619 0.00 0.00 0.00 3.33
39 40 0.692476 CCCCTCACAGACACCAATGA 59.308 55.000 0.00 0.00 0.00 2.57
89 90 6.273071 GGATGAGCGTATGTGCATATGTATA 58.727 40.000 6.16 0.00 37.31 1.47
106 107 0.099436 GTGCGTTCATTGGGATGAGC 59.901 55.000 0.00 0.00 42.90 4.26
141 146 4.046938 TCAGTTTCTCGGATATGCTCAC 57.953 45.455 0.00 0.00 0.00 3.51
149 154 0.173708 GTCGGCTCAGTTTCTCGGAT 59.826 55.000 0.00 0.00 0.00 4.18
170 175 6.637254 GCGACTTCGTCAATCTTAAGATGATA 59.363 38.462 18.61 4.82 42.22 2.15
274 279 2.553602 TGACACTGATGCTCGCATTTTT 59.446 40.909 5.79 0.00 36.70 1.94
288 293 5.651387 TCCAGATTCTAGACTTGACACTG 57.349 43.478 0.00 10.34 0.00 3.66
390 396 2.158143 ACCAGGGTTCAAGTCCTAGACT 60.158 50.000 0.00 0.00 45.64 3.24
468 474 5.272283 TGTATCGACCATAGAAAAGGGAC 57.728 43.478 0.00 0.00 0.00 4.46
493 499 2.761208 GCCGCATGTCTAGGGAGTATAT 59.239 50.000 0.00 0.00 0.00 0.86
526 532 3.243602 ACGGAACTAACAAAATGGTTGCC 60.244 43.478 0.00 0.00 32.29 4.52
571 577 6.111382 TCCAAATATTCAACTGAGAGCTCTG 58.889 40.000 23.91 10.55 35.10 3.35
572 578 6.305272 TCCAAATATTCAACTGAGAGCTCT 57.695 37.500 18.28 18.28 0.00 4.09
660 667 4.040339 CCCCATCAAATATAAACTTGCCCC 59.960 45.833 0.00 0.00 0.00 5.80
717 2759 9.204570 GTAGCACAAAAGAAATCTGTCTAGTTA 57.795 33.333 0.00 0.00 0.00 2.24
767 3349 4.043100 GTTTGGGCCGGGCTACCT 62.043 66.667 28.80 0.00 33.28 3.08
933 3521 2.830370 CCGGATGCCTTCAAGCCC 60.830 66.667 0.00 0.00 0.00 5.19
940 3528 2.369394 GTCTCAAATTCCGGATGCCTT 58.631 47.619 4.15 0.00 0.00 4.35
1030 3630 2.119484 TTTGGATCGGTTGGAGGCGT 62.119 55.000 0.00 0.00 0.00 5.68
1102 3702 0.876342 CCTTCCGCACGGAGAATAGC 60.876 60.000 12.15 0.00 46.06 2.97
1104 3704 1.134907 GTTCCTTCCGCACGGAGAATA 60.135 52.381 12.15 0.00 46.06 1.75
1211 3829 0.538584 TGATCATCTTCGGCTGCACT 59.461 50.000 0.50 0.00 0.00 4.40
1540 6629 7.856145 AAGATTGCTTGAGTACTTGATAAGG 57.144 36.000 0.00 0.00 31.83 2.69
1570 6659 7.278868 TGAAATGCAGTTTTTACGAAACCAAAT 59.721 29.630 0.00 0.00 0.00 2.32
1598 6687 6.758886 GGTTATGTTCTTCATCTCTACACCAG 59.241 42.308 0.00 0.00 37.91 4.00
1647 6744 7.493971 ACATGTGCAGAGCTATTAAAACTAGAG 59.506 37.037 0.00 0.00 0.00 2.43
1649 6746 7.278646 TCACATGTGCAGAGCTATTAAAACTAG 59.721 37.037 21.38 0.00 0.00 2.57
1747 6844 2.082140 TCCTATACACCAGCACGGAT 57.918 50.000 0.00 0.00 38.63 4.18
1754 6851 7.238486 AGCTGAATAGAATCCTATACACCAG 57.762 40.000 0.00 0.00 34.63 4.00
2024 7122 4.594920 AGATCAACTCCTGAAACTTGAGGA 59.405 41.667 0.00 0.00 38.29 3.71
2192 7293 2.677228 CCAGGCTTTGATCCCGGT 59.323 61.111 0.00 0.00 0.00 5.28
2225 7329 2.375146 GATTACCCCATTGTCACCCAC 58.625 52.381 0.00 0.00 0.00 4.61
2243 7347 2.507944 GAGCCACCTGCATCCGAT 59.492 61.111 0.00 0.00 44.83 4.18
2351 7455 7.204604 TGCTCATGCCAAAAACATATGATAAG 58.795 34.615 10.38 0.00 38.71 1.73
2353 7457 6.712179 TGCTCATGCCAAAAACATATGATA 57.288 33.333 10.38 0.00 38.71 2.15
2365 7469 7.565323 AAAAATTTAAACTTGCTCATGCCAA 57.435 28.000 0.00 0.00 38.71 4.52
2391 7495 0.254747 TTGATTGAGCCTAACGGGGG 59.745 55.000 0.00 0.00 35.12 5.40
2434 7538 2.030562 CAAAGCTCCCGTCCGTGT 59.969 61.111 0.00 0.00 0.00 4.49
2435 7539 3.423154 GCAAAGCTCCCGTCCGTG 61.423 66.667 0.00 0.00 0.00 4.94
2440 7544 2.594592 GTGGTGCAAAGCTCCCGT 60.595 61.111 7.54 0.00 40.96 5.28
2481 7585 4.785453 GGGCGAGCTGGTTGAGGG 62.785 72.222 0.00 0.00 0.00 4.30
2486 7590 2.925170 AGTGAGGGCGAGCTGGTT 60.925 61.111 0.00 0.00 0.00 3.67
2497 7601 6.716934 TTTCTAAGGATAGCTACAGTGAGG 57.283 41.667 0.00 0.00 0.00 3.86
2513 7617 4.120589 GTGGCGAGGATACCTTTTCTAAG 58.879 47.826 0.00 0.00 31.76 2.18
2515 7619 2.433239 GGTGGCGAGGATACCTTTTCTA 59.567 50.000 0.00 0.00 31.76 2.10
2525 7629 0.765903 ATCCTGATGGTGGCGAGGAT 60.766 55.000 0.00 0.00 39.98 3.24
2538 7642 1.781786 GAGACTAGTGGCCATCCTGA 58.218 55.000 9.72 0.00 0.00 3.86
2539 7643 0.387202 CGAGACTAGTGGCCATCCTG 59.613 60.000 9.72 2.23 0.00 3.86
2540 7644 0.033011 ACGAGACTAGTGGCCATCCT 60.033 55.000 9.72 4.55 0.00 3.24
2541 7645 0.386113 GACGAGACTAGTGGCCATCC 59.614 60.000 9.72 0.00 0.00 3.51
2542 7646 0.029567 CGACGAGACTAGTGGCCATC 59.970 60.000 9.72 1.23 0.00 3.51
2543 7647 1.384989 CCGACGAGACTAGTGGCCAT 61.385 60.000 9.72 0.00 0.00 4.40
2544 7648 2.044555 CCGACGAGACTAGTGGCCA 61.045 63.158 0.00 0.00 0.00 5.36
2547 7651 1.018226 ACGTCCGACGAGACTAGTGG 61.018 60.000 27.03 0.00 46.05 4.00
2549 7653 2.266554 CTTACGTCCGACGAGACTAGT 58.733 52.381 27.03 5.60 46.05 2.57
2551 7655 1.002366 GCTTACGTCCGACGAGACTA 58.998 55.000 27.03 6.42 46.05 2.59
2588 7692 2.418910 CCACGAGCCTCAGACCGAT 61.419 63.158 0.00 0.00 0.00 4.18
2734 7838 1.341156 GGGTGCAGCTAGAGGTGGAT 61.341 60.000 16.65 0.00 45.06 3.41
3069 8176 4.796038 GGTAACTACCACTGCTTGTAGA 57.204 45.455 0.80 0.00 45.73 2.59


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

AutoCloner maintained by Alex Coulton.