Multiple sequence alignment - TraesCS2D01G138700

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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 TraesCS2D01G138700 chr2D 100.000 6245 0 0 1 6245 81660332 81654088 0.000000e+00 11533.0
1 TraesCS2D01G138700 chr2D 91.837 98 7 1 5273 5370 466691662 466691566 1.090000e-27 135.0
2 TraesCS2D01G138700 chr2D 97.059 34 0 1 5369 5402 299654784 299654816 8.750000e-04 56.5
3 TraesCS2D01G138700 chr2A 94.100 5339 203 38 2 5269 139517400 139522697 0.000000e+00 8011.0
4 TraesCS2D01G138700 chr2A 96.552 58 2 0 156 213 139517620 139517677 5.150000e-16 97.1
5 TraesCS2D01G138700 chr2A 90.909 44 3 1 5359 5401 363368879 363368836 2.430000e-04 58.4
6 TraesCS2D01G138700 chr2B 89.799 3137 261 32 1107 4209 155176905 155173794 0.000000e+00 3965.0
7 TraesCS2D01G138700 chr2B 89.330 881 74 14 212 1075 155177775 155176898 0.000000e+00 1088.0
8 TraesCS2D01G138700 chr2B 93.160 614 38 3 4656 5269 155159307 155158698 0.000000e+00 898.0
9 TraesCS2D01G138700 chr2B 87.288 472 33 8 4206 4654 155159807 155159340 1.200000e-141 514.0
10 TraesCS2D01G138700 chr2B 94.860 214 9 2 1 213 155177938 155177726 3.610000e-87 333.0
11 TraesCS2D01G138700 chr5A 84.106 3580 382 96 1104 4582 87896254 87892761 0.000000e+00 3286.0
12 TraesCS2D01G138700 chr5A 81.931 2983 384 80 1104 4017 87430506 87427610 0.000000e+00 2379.0
13 TraesCS2D01G138700 chr5A 85.075 938 96 22 212 1131 87897270 87896359 0.000000e+00 917.0
14 TraesCS2D01G138700 chr5A 87.321 560 55 6 4715 5269 87891725 87891177 1.480000e-175 627.0
15 TraesCS2D01G138700 chr5A 89.958 478 46 2 4793 5269 87427073 87426597 3.200000e-172 616.0
16 TraesCS2D01G138700 chr5A 83.835 532 67 14 212 731 87431460 87430936 7.280000e-134 488.0
17 TraesCS2D01G138700 chr5A 89.918 367 32 4 773 1136 87430935 87430571 9.480000e-128 468.0
18 TraesCS2D01G138700 chr5A 85.749 407 50 3 4056 4456 87427529 87427125 2.080000e-114 424.0
19 TraesCS2D01G138700 chr5A 86.058 208 27 2 1 207 87431622 87431416 8.150000e-54 222.0
20 TraesCS2D01G138700 chr5A 85.976 164 17 3 50 213 87897378 87897221 2.990000e-38 171.0
21 TraesCS2D01G138700 chr5B 81.209 2762 401 58 1313 4017 101155129 101152429 0.000000e+00 2117.0
22 TraesCS2D01G138700 chr5B 79.021 2226 344 74 447 2609 364799761 364797596 0.000000e+00 1410.0
23 TraesCS2D01G138700 chr5B 80.561 1533 226 37 3046 4542 364797333 364795837 0.000000e+00 1114.0
24 TraesCS2D01G138700 chr5B 89.387 914 50 18 5368 6245 2052354 2053256 0.000000e+00 1107.0
25 TraesCS2D01G138700 chr5B 89.641 473 45 2 4797 5266 101151759 101151288 3.220000e-167 599.0
26 TraesCS2D01G138700 chr5B 84.919 557 74 7 4715 5269 364795777 364795229 7.070000e-154 555.0
27 TraesCS2D01G138700 chr5B 83.427 531 70 15 212 731 101230292 101229769 1.580000e-130 477.0
28 TraesCS2D01G138700 chr5B 87.978 366 40 3 773 1136 101229768 101229405 4.470000e-116 429.0
29 TraesCS2D01G138700 chr5B 86.469 303 38 2 4154 4456 101152114 101151815 4.670000e-86 329.0
30 TraesCS2D01G138700 chr5B 88.372 215 17 2 1104 1310 101229298 101229084 1.040000e-62 252.0
31 TraesCS2D01G138700 chr5B 95.000 40 1 1 5369 5408 697961077 697961115 1.880000e-05 62.1
32 TraesCS2D01G138700 chr5D 81.530 2615 340 62 1104 3644 93990280 93987735 0.000000e+00 2021.0
33 TraesCS2D01G138700 chr5D 89.891 366 33 3 773 1136 93990719 93990356 9.480000e-128 468.0
34 TraesCS2D01G138700 chr5D 82.959 534 65 21 212 731 93991241 93990720 5.710000e-125 459.0
35 TraesCS2D01G138700 chr5D 86.473 207 26 2 1 207 93991403 93991199 6.300000e-55 226.0
36 TraesCS2D01G138700 chr6B 89.421 898 60 9 5370 6245 564363335 564364219 0.000000e+00 1099.0
37 TraesCS2D01G138700 chr6B 88.182 110 10 3 5263 5371 131284819 131284712 1.830000e-25 128.0
38 TraesCS2D01G138700 chr6B 97.368 38 1 0 2658 2695 95494817 95494854 1.450000e-06 65.8
39 TraesCS2D01G138700 chr1A 90.265 113 8 3 5261 5371 492648659 492648548 1.810000e-30 145.0
40 TraesCS2D01G138700 chr1A 89.815 108 8 2 5263 5370 291679052 291678948 1.090000e-27 135.0
41 TraesCS2D01G138700 chr1A 95.122 41 1 1 5368 5408 17519166 17519205 5.230000e-06 63.9
42 TraesCS2D01G138700 chr4D 94.505 91 5 0 5280 5370 105244448 105244538 2.350000e-29 141.0
43 TraesCS2D01G138700 chr4D 90.909 44 1 3 5360 5401 80714432 80714390 8.750000e-04 56.5
44 TraesCS2D01G138700 chr3A 93.548 93 6 0 5278 5370 184663623 184663531 8.440000e-29 139.0
45 TraesCS2D01G138700 chr3A 93.617 94 5 1 5278 5370 553031328 553031421 8.440000e-29 139.0
46 TraesCS2D01G138700 chr3A 86.250 80 5 4 2616 2695 109148679 109148752 1.440000e-11 82.4
47 TraesCS2D01G138700 chr3A 82.500 80 5 5 2617 2696 699881925 699881855 1.880000e-05 62.1
48 TraesCS2D01G138700 chr3A 94.872 39 1 1 5370 5408 495996077 495996114 6.760000e-05 60.2
49 TraesCS2D01G138700 chr7A 91.919 99 7 1 5272 5370 455703274 455703177 3.040000e-28 137.0
50 TraesCS2D01G138700 chr7A 92.857 42 2 1 2658 2698 262465915 262465956 6.760000e-05 60.2
51 TraesCS2D01G138700 chr6A 89.091 110 8 3 5262 5370 145996675 145996781 3.930000e-27 134.0
52 TraesCS2D01G138700 chr7B 93.182 44 2 1 2658 2700 242718363 242718320 5.230000e-06 63.9
53 TraesCS2D01G138700 chr7B 97.059 34 1 0 5368 5401 355849444 355849411 2.430000e-04 58.4
54 TraesCS2D01G138700 chr3D 94.737 38 2 0 2659 2696 115025342 115025305 6.760000e-05 60.2


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 TraesCS2D01G138700 chr2D 81654088 81660332 6244 True 11533.000000 11533 100.000000 1 6245 1 chr2D.!!$R1 6244
1 TraesCS2D01G138700 chr2A 139517400 139522697 5297 False 8011.000000 8011 94.100000 2 5269 1 chr2A.!!$F1 5267
2 TraesCS2D01G138700 chr2B 155173794 155177938 4144 True 1795.333333 3965 91.329667 1 4209 3 chr2B.!!$R2 4208
3 TraesCS2D01G138700 chr2B 155158698 155159807 1109 True 706.000000 898 90.224000 4206 5269 2 chr2B.!!$R1 1063
4 TraesCS2D01G138700 chr5A 87891177 87897378 6201 True 1250.250000 3286 85.619500 50 5269 4 chr5A.!!$R2 5219
5 TraesCS2D01G138700 chr5A 87426597 87431622 5025 True 766.166667 2379 86.241500 1 5269 6 chr5A.!!$R1 5268
6 TraesCS2D01G138700 chr5B 2052354 2053256 902 False 1107.000000 1107 89.387000 5368 6245 1 chr5B.!!$F1 877
7 TraesCS2D01G138700 chr5B 364795229 364799761 4532 True 1026.333333 1410 81.500333 447 5269 3 chr5B.!!$R3 4822
8 TraesCS2D01G138700 chr5B 101151288 101155129 3841 True 1015.000000 2117 85.773000 1313 5266 3 chr5B.!!$R1 3953
9 TraesCS2D01G138700 chr5B 101229084 101230292 1208 True 386.000000 477 86.592333 212 1310 3 chr5B.!!$R2 1098
10 TraesCS2D01G138700 chr5D 93987735 93991403 3668 True 793.500000 2021 85.213250 1 3644 4 chr5D.!!$R1 3643
11 TraesCS2D01G138700 chr6B 564363335 564364219 884 False 1099.000000 1099 89.421000 5370 6245 1 chr6B.!!$F2 875

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
929 973 1.145738 GTCATGCCACCCCTATCCAAT 59.854 52.381 0.00 0.0 0.00 3.16 F
948 992 1.167851 TCAACACGTAGTCTACCCCG 58.832 55.000 4.39 0.0 41.61 5.73 F
1294 1499 3.093057 AGCGGTCTCACTTCAGTAGATT 58.907 45.455 0.00 0.0 0.00 2.40 F
1800 2041 5.163109 TGCCCCTTTCATTCTTTGGAAATTT 60.163 36.000 0.00 0.0 34.90 1.82 F
3132 3449 3.949754 TCCGTCTGTGATAATACGTCCTT 59.050 43.478 0.00 0.0 33.63 3.36 F
4105 4752 2.874849 AGGCAAATATTTTCCGCAACG 58.125 42.857 10.67 0.0 0.00 4.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2388 2638 2.870411 AGCTAACACAAACGAGGTTGAC 59.130 45.455 7.97 0.00 32.59 3.18 R
2613 2877 4.202245 TCGGATTTGAAGGGAGTACTTG 57.798 45.455 0.00 0.00 0.00 3.16 R
3023 3336 5.017490 ACTACACCCTCCGATCCATATTAG 58.983 45.833 0.00 0.00 0.00 1.73 R
3346 3688 4.255301 ACTACACTCTTAGACCTCTCACG 58.745 47.826 0.00 0.00 0.00 4.35 R
4503 5163 0.642291 CAAGCATACACGAGTCGCAG 59.358 55.000 13.59 8.31 0.00 5.18 R
5899 7624 0.608130 CCACTCTGGAATCGACCACA 59.392 55.000 0.00 0.00 40.96 4.17 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
187 189 7.382110 TGCATCTAAGGAAGTGATATCTTAGC 58.618 38.462 3.98 0.00 38.80 3.09
224 247 3.282021 TCAACATGGCATCTAAGGAAGC 58.718 45.455 0.00 0.00 35.68 3.86
473 500 4.338964 TGTGCATATCTTTGTAATGGCCTG 59.661 41.667 3.32 0.00 0.00 4.85
610 650 6.769512 TGCATTTATTGAGGGGATAGAGTAC 58.230 40.000 0.00 0.00 0.00 2.73
665 706 4.114794 GCTTGACAAGTGTTTTGCATCTT 58.885 39.130 16.39 0.00 0.00 2.40
682 723 4.781071 CATCTTCAACTCACTTGACAAGC 58.219 43.478 15.24 0.00 38.70 4.01
685 726 3.446310 TCAACTCACTTGACAAGCGTA 57.554 42.857 15.24 0.19 33.65 4.42
929 973 1.145738 GTCATGCCACCCCTATCCAAT 59.854 52.381 0.00 0.00 0.00 3.16
946 990 3.194116 TCCAATCAACACGTAGTCTACCC 59.806 47.826 4.39 0.00 41.61 3.69
948 992 1.167851 TCAACACGTAGTCTACCCCG 58.832 55.000 4.39 0.00 41.61 5.73
1027 1079 4.884164 GGATTGGAAGAACTTCAGGTATGG 59.116 45.833 15.02 0.00 41.20 2.74
1294 1499 3.093057 AGCGGTCTCACTTCAGTAGATT 58.907 45.455 0.00 0.00 0.00 2.40
1301 1506 7.255277 CGGTCTCACTTCAGTAGATTCATATGA 60.255 40.741 0.00 0.00 0.00 2.15
1388 1595 7.425224 AGAGCTATGCTTTCTCTAGGTTAAA 57.575 36.000 0.00 0.00 39.88 1.52
1413 1620 7.801893 TCTTGTATTCAGTAAGGTTTAGGGA 57.198 36.000 0.00 0.00 0.00 4.20
1800 2041 5.163109 TGCCCCTTTCATTCTTTGGAAATTT 60.163 36.000 0.00 0.00 34.90 1.82
1940 2186 7.973048 AATAGTTGGAAGTACAGATACCTCA 57.027 36.000 0.00 0.00 30.88 3.86
2091 2340 5.470098 GTGAGTCATCTTTGTTGGAAGCTTA 59.530 40.000 0.00 0.00 0.00 3.09
2388 2638 6.142818 TGACAGTTTTTAACATCACCAAGG 57.857 37.500 0.00 0.00 0.00 3.61
2539 2803 9.942850 CTAAATTTATCCAAAACAAGGGTCAAT 57.057 29.630 0.00 0.00 0.00 2.57
2566 2830 5.830991 TGGTCTGCCAATGGGTTATAAATAC 59.169 40.000 0.00 0.00 42.83 1.89
2613 2877 8.470657 AGCCTCTTTATAATTCCAAAGATTCC 57.529 34.615 12.38 6.58 39.40 3.01
2848 3127 8.967664 AGTACAAGTTTCTTGTATTGTAACCA 57.032 30.769 20.21 0.39 39.20 3.67
2957 3244 5.916318 AGGACGATATATACTACTCCCTCG 58.084 45.833 0.00 0.00 0.00 4.63
3023 3336 5.065090 ACCTTTGTACTAAACCAACGTCAAC 59.935 40.000 0.00 0.00 0.00 3.18
3041 3354 4.283722 GTCAACTAATATGGATCGGAGGGT 59.716 45.833 0.00 0.00 0.00 4.34
3127 3444 8.395633 TGACATATATCCGTCTGTGATAATACG 58.604 37.037 5.17 0.00 33.18 3.06
3132 3449 3.949754 TCCGTCTGTGATAATACGTCCTT 59.050 43.478 0.00 0.00 33.63 3.36
3330 3671 8.448615 CACATCATTCGATAGTGCATGATATTT 58.551 33.333 7.50 0.00 37.00 1.40
3509 3860 7.330208 CGAGTTAAAATAGGTATATGGGGTTCG 59.670 40.741 0.00 0.00 0.00 3.95
3580 3934 6.552725 AGCACTGATGATCAAGATAAGACCTA 59.447 38.462 0.00 0.00 0.00 3.08
3676 4030 8.421002 ACTCAAGCACTACCACAAAATAAAAAT 58.579 29.630 0.00 0.00 0.00 1.82
4024 4668 6.604795 ACGCCCTTTACTACTACTCTCATAAA 59.395 38.462 0.00 0.00 0.00 1.40
4028 4672 9.680315 CCCTTTACTACTACTCTCATAAAATCG 57.320 37.037 0.00 0.00 0.00 3.34
4105 4752 2.874849 AGGCAAATATTTTCCGCAACG 58.125 42.857 10.67 0.00 0.00 4.10
4115 4762 4.932851 TTTTCCGCAACGTAAAAATTCG 57.067 36.364 0.00 0.00 0.00 3.34
4405 5060 4.649218 TCTTAGCACAGGATACATGTAGCA 59.351 41.667 21.76 0.00 41.41 3.49
4503 5163 9.780186 AGCTGGATAATAGTTCTTAATGTTACC 57.220 33.333 0.00 0.00 0.00 2.85
4976 6675 1.148446 ACTGTATGGTATAGCCCCCGA 59.852 52.381 0.00 0.00 36.04 5.14
5172 6871 1.888512 AGGCCAGCATGTTACAAAGTG 59.111 47.619 5.01 0.00 0.00 3.16
5269 6968 8.951954 ACGAGTATCACTTGTCGAATATAATC 57.048 34.615 0.00 0.00 38.42 1.75
5270 6969 8.784994 ACGAGTATCACTTGTCGAATATAATCT 58.215 33.333 0.00 0.00 38.42 2.40
5271 6970 9.613957 CGAGTATCACTTGTCGAATATAATCTT 57.386 33.333 0.00 0.00 34.28 2.40
5278 6977 9.922305 CACTTGTCGAATATAATCTTTTTCTCC 57.078 33.333 0.00 0.00 0.00 3.71
5279 6978 9.892130 ACTTGTCGAATATAATCTTTTTCTCCT 57.108 29.630 0.00 0.00 0.00 3.69
5294 6993 8.889717 TCTTTTTCTCCTAATAATAAAGCACGG 58.110 33.333 0.00 0.00 0.00 4.94
5295 6994 8.795842 TTTTTCTCCTAATAATAAAGCACGGA 57.204 30.769 0.00 0.00 0.00 4.69
5296 6995 8.974060 TTTTCTCCTAATAATAAAGCACGGAT 57.026 30.769 0.00 0.00 0.00 4.18
5297 6996 8.974060 TTTCTCCTAATAATAAAGCACGGATT 57.026 30.769 0.00 0.00 0.00 3.01
5298 6997 7.962964 TCTCCTAATAATAAAGCACGGATTG 57.037 36.000 0.00 0.00 0.00 2.67
5299 6998 7.732025 TCTCCTAATAATAAAGCACGGATTGA 58.268 34.615 0.00 0.00 0.00 2.57
5300 6999 7.656137 TCTCCTAATAATAAAGCACGGATTGAC 59.344 37.037 0.00 0.00 0.00 3.18
5301 7000 7.506114 TCCTAATAATAAAGCACGGATTGACT 58.494 34.615 0.00 0.00 0.00 3.41
5302 7001 7.656137 TCCTAATAATAAAGCACGGATTGACTC 59.344 37.037 0.00 0.00 0.00 3.36
5303 7002 7.657761 CCTAATAATAAAGCACGGATTGACTCT 59.342 37.037 0.00 0.00 0.00 3.24
5304 7003 6.851222 ATAATAAAGCACGGATTGACTCTG 57.149 37.500 0.00 0.00 36.23 3.35
5305 7004 2.550830 AAAGCACGGATTGACTCTGT 57.449 45.000 0.00 0.00 44.66 3.41
5311 7010 3.753294 ACGGATTGACTCTGTGAGTTT 57.247 42.857 1.58 0.00 43.53 2.66
5312 7011 4.866508 ACGGATTGACTCTGTGAGTTTA 57.133 40.909 1.58 0.00 43.53 2.01
5313 7012 4.557205 ACGGATTGACTCTGTGAGTTTAC 58.443 43.478 1.58 0.00 43.53 2.01
5314 7013 3.927142 CGGATTGACTCTGTGAGTTTACC 59.073 47.826 1.58 3.78 43.53 2.85
5315 7014 3.927142 GGATTGACTCTGTGAGTTTACCG 59.073 47.826 1.58 0.00 43.53 4.02
5316 7015 4.557205 GATTGACTCTGTGAGTTTACCGT 58.443 43.478 1.58 0.00 43.53 4.83
5317 7016 3.637998 TGACTCTGTGAGTTTACCGTC 57.362 47.619 1.58 0.00 43.53 4.79
5318 7017 2.953648 TGACTCTGTGAGTTTACCGTCA 59.046 45.455 1.58 0.00 43.53 4.35
5319 7018 3.243301 TGACTCTGTGAGTTTACCGTCAC 60.243 47.826 1.58 0.00 43.53 3.67
5325 7024 4.557276 GTGAGTTTACCGTCACAATACG 57.443 45.455 0.00 0.00 42.31 3.06
5326 7025 2.988493 TGAGTTTACCGTCACAATACGC 59.012 45.455 0.00 0.00 41.51 4.42
5327 7026 3.248266 GAGTTTACCGTCACAATACGCT 58.752 45.455 0.00 0.00 41.51 5.07
5328 7027 3.656559 AGTTTACCGTCACAATACGCTT 58.343 40.909 0.00 0.00 41.51 4.68
5329 7028 3.676646 AGTTTACCGTCACAATACGCTTC 59.323 43.478 0.00 0.00 41.51 3.86
5330 7029 3.581024 TTACCGTCACAATACGCTTCT 57.419 42.857 0.00 0.00 41.51 2.85
5331 7030 2.450609 ACCGTCACAATACGCTTCTT 57.549 45.000 0.00 0.00 41.51 2.52
5332 7031 2.762745 ACCGTCACAATACGCTTCTTT 58.237 42.857 0.00 0.00 41.51 2.52
5333 7032 2.735134 ACCGTCACAATACGCTTCTTTC 59.265 45.455 0.00 0.00 41.51 2.62
5334 7033 2.993899 CCGTCACAATACGCTTCTTTCT 59.006 45.455 0.00 0.00 41.51 2.52
5335 7034 3.181530 CCGTCACAATACGCTTCTTTCTG 60.182 47.826 0.00 0.00 41.51 3.02
5336 7035 3.428870 CGTCACAATACGCTTCTTTCTGT 59.571 43.478 0.00 0.00 35.87 3.41
5337 7036 4.664139 CGTCACAATACGCTTCTTTCTGTG 60.664 45.833 0.00 0.00 35.87 3.66
5338 7037 4.447724 GTCACAATACGCTTCTTTCTGTGA 59.552 41.667 0.00 0.00 39.36 3.58
5339 7038 5.050363 GTCACAATACGCTTCTTTCTGTGAA 60.050 40.000 3.75 0.00 42.22 3.18
5340 7039 5.700832 TCACAATACGCTTCTTTCTGTGAAT 59.299 36.000 0.00 0.00 38.88 2.57
5341 7040 6.204688 TCACAATACGCTTCTTTCTGTGAATT 59.795 34.615 0.00 0.00 38.88 2.17
5342 7041 6.857964 CACAATACGCTTCTTTCTGTGAATTT 59.142 34.615 0.00 0.00 35.78 1.82
5343 7042 8.015087 CACAATACGCTTCTTTCTGTGAATTTA 58.985 33.333 0.00 0.00 35.78 1.40
5344 7043 8.015658 ACAATACGCTTCTTTCTGTGAATTTAC 58.984 33.333 0.00 0.00 0.00 2.01
5345 7044 5.018695 ACGCTTCTTTCTGTGAATTTACG 57.981 39.130 0.00 0.00 0.00 3.18
5346 7045 3.840763 CGCTTCTTTCTGTGAATTTACGC 59.159 43.478 0.00 0.00 0.00 4.42
5347 7046 4.377431 CGCTTCTTTCTGTGAATTTACGCT 60.377 41.667 0.00 0.00 0.00 5.07
5348 7047 5.452777 GCTTCTTTCTGTGAATTTACGCTT 58.547 37.500 0.00 0.00 0.00 4.68
5349 7048 5.915196 GCTTCTTTCTGTGAATTTACGCTTT 59.085 36.000 0.00 0.00 0.00 3.51
5350 7049 6.086896 GCTTCTTTCTGTGAATTTACGCTTTC 59.913 38.462 0.00 0.00 0.00 2.62
5351 7050 6.612247 TCTTTCTGTGAATTTACGCTTTCA 57.388 33.333 0.00 0.00 0.00 2.69
5532 7234 8.819974 GTTCATGATTTTGACTTGTTCAACAAT 58.180 29.630 2.71 0.00 44.28 2.71
5533 7235 8.945481 TCATGATTTTGACTTGTTCAACAATT 57.055 26.923 2.71 0.00 44.28 2.32
5534 7236 9.381033 TCATGATTTTGACTTGTTCAACAATTT 57.619 25.926 2.71 0.00 44.28 1.82
5535 7237 9.640974 CATGATTTTGACTTGTTCAACAATTTC 57.359 29.630 2.71 4.38 44.28 2.17
5536 7238 9.603921 ATGATTTTGACTTGTTCAACAATTTCT 57.396 25.926 2.71 0.00 44.28 2.52
5606 7310 5.622770 ATTTACGATTTTGAGTGGGTCAC 57.377 39.130 0.00 0.00 33.71 3.67
5617 7321 7.595819 TTTGAGTGGGTCACTAATTTTTCAT 57.404 32.000 0.11 0.00 45.44 2.57
5775 7479 5.355596 CATGTCTACAGTCTCCTTTCATCC 58.644 45.833 0.00 0.00 0.00 3.51
5790 7494 6.594159 TCCTTTCATCCGTGTCTTCTATTTTC 59.406 38.462 0.00 0.00 0.00 2.29
5791 7495 6.371548 CCTTTCATCCGTGTCTTCTATTTTCA 59.628 38.462 0.00 0.00 0.00 2.69
5792 7496 7.094805 CCTTTCATCCGTGTCTTCTATTTTCAA 60.095 37.037 0.00 0.00 0.00 2.69
5793 7497 6.721571 TCATCCGTGTCTTCTATTTTCAAC 57.278 37.500 0.00 0.00 0.00 3.18
5794 7498 6.227522 TCATCCGTGTCTTCTATTTTCAACA 58.772 36.000 0.00 0.00 0.00 3.33
5868 7593 2.732016 CCTCGACAACGGTGGTCA 59.268 61.111 15.59 2.67 40.21 4.02
5881 7606 3.071312 ACGGTGGTCATGTTGTTTACCTA 59.929 43.478 0.00 0.00 32.99 3.08
5899 7624 9.705290 GTTTACCTAATCAAAACATGTTGGAAT 57.295 29.630 12.82 8.85 34.12 3.01
6012 7739 3.258622 TCTCGTCGAGCTAGATATGAGGA 59.741 47.826 17.61 0.00 0.00 3.71
6104 7832 3.243907 GGTTGCACTCTGTGAACTACTCT 60.244 47.826 1.52 0.00 35.23 3.24
6133 7861 7.579146 CGCCTAGTCTATACACCTATCTACTCA 60.579 44.444 0.00 0.00 0.00 3.41
6150 7886 4.240881 ACTCATGCACCAAGTCCATATT 57.759 40.909 0.00 0.00 0.00 1.28
6151 7887 5.372343 ACTCATGCACCAAGTCCATATTA 57.628 39.130 0.00 0.00 0.00 0.98
6162 7898 3.460825 AGTCCATATTACGCCCCCATAT 58.539 45.455 0.00 0.00 0.00 1.78
6166 7902 3.951680 CCATATTACGCCCCCATATTTCC 59.048 47.826 0.00 0.00 0.00 3.13
6226 7962 2.660064 GGGAGGGTGAGTCATGCGT 61.660 63.158 0.00 0.00 0.00 5.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
198 200 6.191657 TCCTTAGATGCCATGTTGATATGT 57.808 37.500 0.00 0.00 0.00 2.29
199 201 6.349115 GCTTCCTTAGATGCCATGTTGATATG 60.349 42.308 0.00 0.00 37.23 1.78
247 272 5.882000 GCATGATGGTAGCCATGTTGATATA 59.118 40.000 5.27 0.00 45.26 0.86
473 500 0.391661 TCAGCGATCACTTCTTGGGC 60.392 55.000 0.00 0.00 0.00 5.36
573 611 9.590451 CCTCAATAAATGCAAGTCAAAACATAT 57.410 29.630 0.00 0.00 0.00 1.78
574 612 8.034215 CCCTCAATAAATGCAAGTCAAAACATA 58.966 33.333 0.00 0.00 0.00 2.29
585 625 6.266131 ACTCTATCCCCTCAATAAATGCAA 57.734 37.500 0.00 0.00 0.00 4.08
610 650 8.412456 AGTGATCTGACACATAATCTAACTCAG 58.588 37.037 11.18 0.00 42.45 3.35
665 706 2.309528 ACGCTTGTCAAGTGAGTTGA 57.690 45.000 28.47 0.00 43.26 3.18
700 741 6.814954 AGACATTTATTCCTCTAGCCAAGA 57.185 37.500 0.00 0.00 0.00 3.02
766 808 2.831685 ACCGCTAGTGATCAAACACA 57.168 45.000 4.44 0.00 42.45 3.72
929 973 1.167851 CGGGGTAGACTACGTGTTGA 58.832 55.000 6.54 0.00 0.00 3.18
946 990 0.248289 TAAAGGGGAAAGAGTCGCGG 59.752 55.000 6.13 0.00 40.09 6.46
948 992 5.448768 GCTTTTATAAAGGGGAAAGAGTCGC 60.449 44.000 9.16 0.00 38.47 5.19
1294 1499 4.495911 TGTTTTGCAAGCGTTCATATGA 57.504 36.364 0.00 0.00 0.00 2.15
1301 1506 1.137872 TCCCATTGTTTTGCAAGCGTT 59.862 42.857 0.00 0.00 40.86 4.84
1388 1595 8.388656 TCCCTAAACCTTACTGAATACAAGAT 57.611 34.615 0.00 0.00 0.00 2.40
1413 1620 8.818622 AATATGCTAGTAATGATCCATGCATT 57.181 30.769 0.00 0.00 39.95 3.56
1766 2000 3.228188 TGAAAGGGGCATATGGTCATC 57.772 47.619 4.56 0.00 0.00 2.92
1940 2186 8.664798 GCACTTTTTATTCAACTTTTGTTCCTT 58.335 29.630 0.00 0.00 41.35 3.36
2056 2305 6.128090 ACAAAGATGACTCACATGCATAACAG 60.128 38.462 0.00 0.00 39.56 3.16
2091 2340 8.772250 TGGAGAACTGGTTGAGAATATTATTCT 58.228 33.333 16.95 16.95 0.00 2.40
2268 2518 4.606457 GACAAGATCCAACTTTGATCCG 57.394 45.455 0.00 0.00 0.00 4.18
2388 2638 2.870411 AGCTAACACAAACGAGGTTGAC 59.130 45.455 7.97 0.00 32.59 3.18
2516 2779 9.639563 AAAATTGACCCTTGTTTTGGATAAATT 57.360 25.926 0.00 0.00 0.00 1.82
2566 2830 5.461737 GCTCGAAACAGAATGAAGATCTAGG 59.538 44.000 0.00 0.00 39.69 3.02
2613 2877 4.202245 TCGGATTTGAAGGGAGTACTTG 57.798 45.455 0.00 0.00 0.00 3.16
3023 3336 5.017490 ACTACACCCTCCGATCCATATTAG 58.983 45.833 0.00 0.00 0.00 1.73
3285 3615 5.309323 TGTGGCACTACAATTAAGAATGC 57.691 39.130 19.83 0.00 0.00 3.56
3330 3671 6.070995 ACCTCTCACGATCAAAGTACCATAAA 60.071 38.462 0.00 0.00 0.00 1.40
3346 3688 4.255301 ACTACACTCTTAGACCTCTCACG 58.745 47.826 0.00 0.00 0.00 4.35
3509 3860 4.458989 TCTTGGGAATGATGTTGTACTTGC 59.541 41.667 0.00 0.00 0.00 4.01
3580 3934 6.057533 TGAAATCCAGCTTCGATCATATTGT 58.942 36.000 0.00 0.00 0.00 2.71
3676 4030 6.849085 ACCTACATCAACCATAATTGCAAA 57.151 33.333 1.71 0.00 0.00 3.68
4024 4668 6.540438 TTCTAGATGGTCTACAAACCGATT 57.460 37.500 0.00 0.00 42.62 3.34
4028 4672 9.832445 TTTGATATTCTAGATGGTCTACAAACC 57.168 33.333 0.00 0.00 39.94 3.27
4062 4708 7.413438 GCCTACACACTCTTATTTCATGAACAG 60.413 40.741 7.89 4.96 0.00 3.16
4105 4752 4.029043 GCAAGAGGCGATCGAATTTTTAC 58.971 43.478 21.57 0.00 0.00 2.01
4432 5087 9.755804 TGCTACATGAATGTTTGAATTTGTTTA 57.244 25.926 0.00 0.00 41.97 2.01
4503 5163 0.642291 CAAGCATACACGAGTCGCAG 59.358 55.000 13.59 8.31 0.00 5.18
4548 5208 9.500785 TGATCCCTTTGTTTCAAAATATTTTCC 57.499 29.630 10.53 0.95 0.00 3.13
4763 6419 9.494271 CTGCAAACAGTGAGTAATATATATGGT 57.506 33.333 0.00 0.00 39.22 3.55
4976 6675 4.523943 TGACAAATCCAAGCAATGCTACTT 59.476 37.500 8.68 0.00 38.25 2.24
5172 6871 2.941453 TAGCATGGAGAACGTCACTC 57.059 50.000 12.37 12.37 0.00 3.51
5269 6968 8.889717 TCCGTGCTTTATTATTAGGAGAAAAAG 58.110 33.333 0.00 0.00 0.00 2.27
5270 6969 8.795842 TCCGTGCTTTATTATTAGGAGAAAAA 57.204 30.769 0.00 0.00 0.00 1.94
5271 6970 8.974060 ATCCGTGCTTTATTATTAGGAGAAAA 57.026 30.769 0.00 0.00 0.00 2.29
5272 6971 8.836413 CAATCCGTGCTTTATTATTAGGAGAAA 58.164 33.333 0.00 0.00 0.00 2.52
5273 6972 8.208224 TCAATCCGTGCTTTATTATTAGGAGAA 58.792 33.333 0.00 0.00 0.00 2.87
5274 6973 7.656137 GTCAATCCGTGCTTTATTATTAGGAGA 59.344 37.037 0.00 0.00 0.00 3.71
5275 6974 7.657761 AGTCAATCCGTGCTTTATTATTAGGAG 59.342 37.037 0.00 0.00 0.00 3.69
5276 6975 7.506114 AGTCAATCCGTGCTTTATTATTAGGA 58.494 34.615 0.00 0.00 0.00 2.94
5277 6976 7.657761 AGAGTCAATCCGTGCTTTATTATTAGG 59.342 37.037 0.00 0.00 0.00 2.69
5278 6977 8.491152 CAGAGTCAATCCGTGCTTTATTATTAG 58.509 37.037 0.00 0.00 0.00 1.73
5279 6978 7.985184 ACAGAGTCAATCCGTGCTTTATTATTA 59.015 33.333 0.00 0.00 0.00 0.98
5280 6979 6.823689 ACAGAGTCAATCCGTGCTTTATTATT 59.176 34.615 0.00 0.00 0.00 1.40
5281 6980 6.258727 CACAGAGTCAATCCGTGCTTTATTAT 59.741 38.462 0.00 0.00 0.00 1.28
5282 6981 5.580691 CACAGAGTCAATCCGTGCTTTATTA 59.419 40.000 0.00 0.00 0.00 0.98
5283 6982 4.393062 CACAGAGTCAATCCGTGCTTTATT 59.607 41.667 0.00 0.00 0.00 1.40
5284 6983 3.935203 CACAGAGTCAATCCGTGCTTTAT 59.065 43.478 0.00 0.00 0.00 1.40
5285 6984 3.006430 TCACAGAGTCAATCCGTGCTTTA 59.994 43.478 0.00 0.00 0.00 1.85
5286 6985 2.146342 CACAGAGTCAATCCGTGCTTT 58.854 47.619 0.00 0.00 0.00 3.51
5287 6986 1.344438 TCACAGAGTCAATCCGTGCTT 59.656 47.619 0.00 0.00 0.00 3.91
5288 6987 0.969149 TCACAGAGTCAATCCGTGCT 59.031 50.000 0.00 0.00 0.00 4.40
5289 6988 1.337260 ACTCACAGAGTCAATCCGTGC 60.337 52.381 0.00 0.00 38.71 5.34
5290 6989 2.732412 ACTCACAGAGTCAATCCGTG 57.268 50.000 0.00 0.00 38.71 4.94
5291 6990 3.753294 AAACTCACAGAGTCAATCCGT 57.247 42.857 0.00 0.00 42.59 4.69
5292 6991 3.927142 GGTAAACTCACAGAGTCAATCCG 59.073 47.826 0.00 0.00 42.59 4.18
5293 6992 3.927142 CGGTAAACTCACAGAGTCAATCC 59.073 47.826 0.00 1.52 42.59 3.01
5294 6993 4.557205 ACGGTAAACTCACAGAGTCAATC 58.443 43.478 0.00 0.00 42.59 2.67
5295 6994 4.038763 TGACGGTAAACTCACAGAGTCAAT 59.961 41.667 0.00 0.00 42.59 2.57
5296 6995 3.382227 TGACGGTAAACTCACAGAGTCAA 59.618 43.478 0.00 0.00 42.59 3.18
5297 6996 2.953648 TGACGGTAAACTCACAGAGTCA 59.046 45.455 0.00 0.00 42.59 3.41
5298 6997 3.243301 TGTGACGGTAAACTCACAGAGTC 60.243 47.826 0.00 0.00 42.59 3.36
5299 6998 2.691526 TGTGACGGTAAACTCACAGAGT 59.308 45.455 0.58 0.00 45.64 3.24
5300 6999 3.364889 TGTGACGGTAAACTCACAGAG 57.635 47.619 0.58 0.00 41.46 3.35
5301 7000 3.804786 TTGTGACGGTAAACTCACAGA 57.195 42.857 4.72 0.00 45.72 3.41
5302 7001 4.089493 CGTATTGTGACGGTAAACTCACAG 59.911 45.833 4.72 0.00 45.72 3.66
5303 7002 3.982701 CGTATTGTGACGGTAAACTCACA 59.017 43.478 0.58 0.58 43.99 3.58
5304 7003 3.181537 GCGTATTGTGACGGTAAACTCAC 60.182 47.826 0.00 0.00 43.13 3.51
5305 7004 2.988493 GCGTATTGTGACGGTAAACTCA 59.012 45.455 0.00 0.00 43.13 3.41
5306 7005 3.629719 GCGTATTGTGACGGTAAACTC 57.370 47.619 0.00 0.00 43.13 3.01
5313 7012 2.993899 AGAAAGAAGCGTATTGTGACGG 59.006 45.455 0.00 0.00 43.13 4.79
5314 7013 3.428870 ACAGAAAGAAGCGTATTGTGACG 59.571 43.478 2.77 0.00 45.70 4.35
5315 7014 4.447724 TCACAGAAAGAAGCGTATTGTGAC 59.552 41.667 0.71 0.00 38.67 3.67
5316 7015 4.627058 TCACAGAAAGAAGCGTATTGTGA 58.373 39.130 0.71 0.71 40.55 3.58
5317 7016 4.990543 TCACAGAAAGAAGCGTATTGTG 57.009 40.909 0.00 0.00 36.64 3.33
5318 7017 6.560253 AATTCACAGAAAGAAGCGTATTGT 57.440 33.333 0.00 0.00 0.00 2.71
5319 7018 7.214449 CGTAAATTCACAGAAAGAAGCGTATTG 59.786 37.037 0.00 0.00 0.00 1.90
5320 7019 7.234384 CGTAAATTCACAGAAAGAAGCGTATT 58.766 34.615 0.00 0.00 0.00 1.89
5321 7020 6.672357 GCGTAAATTCACAGAAAGAAGCGTAT 60.672 38.462 0.00 0.00 0.00 3.06
5322 7021 5.389098 GCGTAAATTCACAGAAAGAAGCGTA 60.389 40.000 0.00 0.00 0.00 4.42
5323 7022 4.610680 GCGTAAATTCACAGAAAGAAGCGT 60.611 41.667 0.00 0.00 0.00 5.07
5324 7023 3.840763 GCGTAAATTCACAGAAAGAAGCG 59.159 43.478 0.00 0.00 0.00 4.68
5325 7024 5.035784 AGCGTAAATTCACAGAAAGAAGC 57.964 39.130 0.00 0.00 0.00 3.86
5326 7025 7.132213 TGAAAGCGTAAATTCACAGAAAGAAG 58.868 34.615 0.00 0.00 30.94 2.85
5327 7026 7.022055 TGAAAGCGTAAATTCACAGAAAGAA 57.978 32.000 0.00 0.00 30.94 2.52
5328 7027 6.612247 TGAAAGCGTAAATTCACAGAAAGA 57.388 33.333 0.00 0.00 30.94 2.52
5359 7058 9.843334 CGGGCATTTTTACTAGTATGTTTTAAA 57.157 29.630 2.79 0.00 0.00 1.52
5360 7059 9.012161 ACGGGCATTTTTACTAGTATGTTTTAA 57.988 29.630 2.79 0.00 0.00 1.52
5361 7060 8.452534 CACGGGCATTTTTACTAGTATGTTTTA 58.547 33.333 2.79 0.00 0.00 1.52
5362 7061 7.309920 CACGGGCATTTTTACTAGTATGTTTT 58.690 34.615 2.79 0.00 0.00 2.43
5363 7062 6.624204 GCACGGGCATTTTTACTAGTATGTTT 60.624 38.462 3.77 0.00 40.72 2.83
5364 7063 5.163693 GCACGGGCATTTTTACTAGTATGTT 60.164 40.000 3.77 0.00 40.72 2.71
5365 7064 4.334481 GCACGGGCATTTTTACTAGTATGT 59.666 41.667 3.77 0.00 40.72 2.29
5366 7065 4.551990 CGCACGGGCATTTTTACTAGTATG 60.552 45.833 11.77 1.08 41.24 2.39
5447 7146 6.875076 GTCTCTAAAATTAGGGAGCACAGTA 58.125 40.000 2.99 0.00 40.74 2.74
5448 7147 5.735766 GTCTCTAAAATTAGGGAGCACAGT 58.264 41.667 2.99 0.00 40.74 3.55
5532 7234 6.889198 TGAGAGAACTCCTTGAGAAAAGAAA 58.111 36.000 0.00 0.00 41.99 2.52
5533 7235 6.485830 TGAGAGAACTCCTTGAGAAAAGAA 57.514 37.500 0.00 0.00 41.99 2.52
5534 7236 6.678568 ATGAGAGAACTCCTTGAGAAAAGA 57.321 37.500 0.00 0.00 41.99 2.52
5535 7237 6.933521 TGAATGAGAGAACTCCTTGAGAAAAG 59.066 38.462 0.00 0.00 41.99 2.27
5536 7238 6.830912 TGAATGAGAGAACTCCTTGAGAAAA 58.169 36.000 0.00 0.00 41.99 2.29
5606 7310 9.649167 AAATGAAAGAGCTCCATGAAAAATTAG 57.351 29.630 10.93 0.00 0.00 1.73
5617 7321 6.779860 ACCTTAACTAAATGAAAGAGCTCCA 58.220 36.000 10.93 1.22 0.00 3.86
5705 7409 1.203065 CGTTGCAACGTACGTGCAT 59.797 52.632 37.16 14.20 46.63 3.96
5706 7410 2.621542 CGTTGCAACGTACGTGCA 59.378 55.556 37.16 28.98 46.63 4.57
5731 7435 5.048846 TGCTTATTGGGATAGGGAGTTTC 57.951 43.478 0.00 0.00 0.00 2.78
5775 7479 6.887368 TGTCATGTTGAAAATAGAAGACACG 58.113 36.000 0.00 0.00 28.13 4.49
5790 7494 6.185852 TGTGCTGAAATAGATGTCATGTTG 57.814 37.500 0.00 0.00 0.00 3.33
5791 7495 6.822667 TTGTGCTGAAATAGATGTCATGTT 57.177 33.333 0.00 0.00 0.00 2.71
5792 7496 7.255035 GCTATTGTGCTGAAATAGATGTCATGT 60.255 37.037 14.11 0.00 39.12 3.21
5793 7497 7.041303 AGCTATTGTGCTGAAATAGATGTCATG 60.041 37.037 14.11 0.00 42.33 3.07
5794 7498 6.996879 AGCTATTGTGCTGAAATAGATGTCAT 59.003 34.615 14.11 0.00 42.33 3.06
5809 7513 0.883833 ACACAGGCAAGCTATTGTGC 59.116 50.000 17.82 9.12 43.50 4.57
5881 7606 5.927819 ACCACATTCCAACATGTTTTGATT 58.072 33.333 8.77 2.72 35.03 2.57
5899 7624 0.608130 CCACTCTGGAATCGACCACA 59.392 55.000 0.00 0.00 40.96 4.17
6012 7739 2.442413 GACTAGCTCATAGAGGGCGAT 58.558 52.381 0.00 0.00 35.30 4.58
6057 7785 5.292765 TCAAATCCAGCTCGATGAGATTAC 58.707 41.667 0.00 0.00 0.00 1.89
6065 7793 1.207791 ACCCTCAAATCCAGCTCGAT 58.792 50.000 0.00 0.00 0.00 3.59
6104 7832 2.662866 AGGTGTATAGACTAGGCGCAA 58.337 47.619 10.83 0.00 0.00 4.85
6133 7861 2.878406 GCGTAATATGGACTTGGTGCAT 59.122 45.455 9.38 9.38 45.84 3.96
6150 7886 1.071814 GCGGAAATATGGGGGCGTA 59.928 57.895 0.00 0.00 0.00 4.42
6151 7887 2.203294 GCGGAAATATGGGGGCGT 60.203 61.111 0.00 0.00 0.00 5.68
6162 7898 2.020720 TGAGTCAAAAGCAAGCGGAAA 58.979 42.857 0.00 0.00 0.00 3.13
6166 7902 4.726416 ACATTATGAGTCAAAAGCAAGCG 58.274 39.130 0.00 0.00 0.00 4.68
6226 7962 4.408821 GAGGCATGCGGGGACACA 62.409 66.667 12.44 0.00 0.00 3.72


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

AutoCloner maintained by Alex Coulton.