Multiple sequence alignment - TraesCS1B01G126000

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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 TraesCS1B01G126000 chr1B 100.000 4560 0 0 1 4560 154147340 154151899 0.000000e+00 8421
1 TraesCS1B01G126000 chr1B 92.529 937 55 8 5 931 55536583 55535652 0.000000e+00 1328
2 TraesCS1B01G126000 chr2A 99.180 4392 33 3 1 4390 195112236 195116626 0.000000e+00 7908
3 TraesCS1B01G126000 chr2A 97.742 2834 59 5 1203 4033 721735602 721738433 0.000000e+00 4874
4 TraesCS1B01G126000 chr2A 98.207 1227 14 4 1 1226 721734352 721735571 0.000000e+00 2137
5 TraesCS1B01G126000 chr2A 95.676 370 15 1 4021 4390 721738447 721738815 1.090000e-165 593
6 TraesCS1B01G126000 chr2A 92.946 241 16 1 4152 4392 281673688 281673927 2.610000e-92 350
7 TraesCS1B01G126000 chr2A 94.915 177 8 1 4384 4560 318598339 318598164 4.490000e-70 276
8 TraesCS1B01G126000 chr1A 98.545 4398 35 15 1 4393 14529380 14525007 0.000000e+00 7740
9 TraesCS1B01G126000 chr1A 89.675 862 56 14 81 931 409841464 409842303 0.000000e+00 1068
10 TraesCS1B01G126000 chr1A 91.808 354 14 7 3403 3741 13765077 13764724 3.190000e-131 479
11 TraesCS1B01G126000 chr7A 96.787 4419 77 9 1 4390 678172323 678167941 0.000000e+00 7313
12 TraesCS1B01G126000 chr7D 97.613 1843 40 2 923 2761 509912572 509910730 0.000000e+00 3157
13 TraesCS1B01G126000 chr7D 94.984 1216 39 7 2765 3959 509910754 509909540 0.000000e+00 1888
14 TraesCS1B01G126000 chr7D 98.389 931 14 1 1 931 509914521 509913592 0.000000e+00 1635
15 TraesCS1B01G126000 chr7D 96.471 170 6 0 4391 4560 222407418 222407587 9.660000e-72 281
16 TraesCS1B01G126000 chr7D 87.500 208 24 2 3753 3959 162188507 162188713 5.900000e-59 239
17 TraesCS1B01G126000 chr7D 85.202 223 7 1 3926 4122 509909543 509909321 5.980000e-49 206
18 TraesCS1B01G126000 chr7D 96.639 119 4 0 4019 4137 501018942 501018824 1.000000e-46 198
19 TraesCS1B01G126000 chr7D 95.181 83 4 0 3943 4025 501019044 501018962 1.030000e-26 132
20 TraesCS1B01G126000 chr5D 97.458 1849 41 4 923 2765 254531932 254530084 0.000000e+00 3149
21 TraesCS1B01G126000 chr5D 97.189 1850 45 5 923 2766 551018687 551016839 0.000000e+00 3121
22 TraesCS1B01G126000 chr5D 94.064 1213 43 9 2765 3955 551016871 551015666 0.000000e+00 1814
23 TraesCS1B01G126000 chr5D 93.527 1205 32 3 2765 3947 254530114 254528934 0.000000e+00 1751
24 TraesCS1B01G126000 chr5D 98.067 931 13 3 1 931 551020632 551019707 0.000000e+00 1615
25 TraesCS1B01G126000 chr5D 98.378 863 12 2 70 931 254533815 254532954 0.000000e+00 1515
26 TraesCS1B01G126000 chr5D 86.275 204 27 1 3753 3955 501350567 501350364 2.140000e-53 220
27 TraesCS1B01G126000 chr5D 96.721 122 4 0 4019 4140 551015496 551015375 2.150000e-48 204
28 TraesCS1B01G126000 chr5D 97.196 107 3 0 3927 4033 551015666 551015560 1.010000e-41 182
29 TraesCS1B01G126000 chr5D 97.115 104 3 0 4019 4122 254528755 254528652 4.690000e-40 176
30 TraesCS1B01G126000 chr5D 94.444 108 6 0 3926 4033 254528926 254528819 2.820000e-37 167
31 TraesCS1B01G126000 chr4D 97.458 1849 41 4 923 2765 40832554 40834402 0.000000e+00 3149
32 TraesCS1B01G126000 chr4D 94.819 1216 41 7 2765 3959 40834372 40835586 0.000000e+00 1877
33 TraesCS1B01G126000 chr4D 97.744 931 13 2 1 931 40830611 40831533 0.000000e+00 1596
34 TraesCS1B01G126000 chr4D 90.602 266 20 5 4138 4402 100763302 100763041 9.390000e-92 348
35 TraesCS1B01G126000 chr4D 96.471 170 6 0 4391 4560 473410971 473411140 9.660000e-72 281
36 TraesCS1B01G126000 chr4D 95.882 170 7 0 4391 4560 99547194 99547363 4.490000e-70 276
37 TraesCS1B01G126000 chr4D 95.882 170 7 0 4391 4560 255682956 255683125 4.490000e-70 276
38 TraesCS1B01G126000 chr4D 95.882 170 7 0 4391 4560 272442732 272442901 4.490000e-70 276
39 TraesCS1B01G126000 chr4D 86.364 220 13 3 3920 4122 40835577 40835796 1.650000e-54 224
40 TraesCS1B01G126000 chrUn 91.889 937 60 9 5 931 315665063 315664133 0.000000e+00 1295
41 TraesCS1B01G126000 chrUn 90.947 950 54 14 5 931 260015956 260015016 0.000000e+00 1249
42 TraesCS1B01G126000 chrUn 90.947 950 54 14 5 931 262120156 262119216 0.000000e+00 1249
43 TraesCS1B01G126000 chrUn 98.044 409 7 1 1311 1718 477629050 477629458 0.000000e+00 710
44 TraesCS1B01G126000 chrUn 99.645 282 1 0 1 282 480831334 480831053 2.430000e-142 516
45 TraesCS1B01G126000 chrUn 86.466 133 12 2 4019 4145 214036641 214036773 1.710000e-29 141
46 TraesCS1B01G126000 chrUn 86.466 133 12 2 4019 4145 235654374 235654506 1.710000e-29 141
47 TraesCS1B01G126000 chrUn 86.466 133 12 2 4019 4145 253139778 253139646 1.710000e-29 141
48 TraesCS1B01G126000 chr4A 90.948 928 73 8 5 931 409027337 409026420 0.000000e+00 1238
49 TraesCS1B01G126000 chr4A 92.913 254 17 1 4137 4390 558667674 558667422 7.210000e-98 368
50 TraesCS1B01G126000 chr3A 90.793 858 58 16 84 931 568016118 568015272 0.000000e+00 1127
51 TraesCS1B01G126000 chr3A 88.060 134 9 2 4019 4145 329532563 329532430 7.900000e-33 152
52 TraesCS1B01G126000 chr3A 98.462 65 1 0 924 988 365952809 365952745 1.040000e-21 115
53 TraesCS1B01G126000 chr6D 96.791 561 17 1 1731 2290 39581154 39580594 0.000000e+00 935
54 TraesCS1B01G126000 chr6D 96.197 447 17 0 2765 3211 39577764 39577318 0.000000e+00 732
55 TraesCS1B01G126000 chr6D 94.627 335 16 1 2283 2615 39578443 39578109 6.760000e-143 518
56 TraesCS1B01G126000 chr6D 96.045 177 6 1 4384 4560 222471402 222471227 2.080000e-73 287
57 TraesCS1B01G126000 chr6D 96.471 170 6 0 4391 4560 75474406 75474575 9.660000e-72 281
58 TraesCS1B01G126000 chr6D 95.882 170 7 0 4391 4560 378343693 378343524 4.490000e-70 276
59 TraesCS1B01G126000 chr6D 96.000 150 4 1 2618 2765 39577883 39577734 4.560000e-60 243
60 TraesCS1B01G126000 chr6D 94.872 78 4 0 1443 1520 39581230 39581153 6.200000e-24 122
61 TraesCS1B01G126000 chr1D 92.023 351 13 4 3406 3741 11620623 11620273 3.190000e-131 479
62 TraesCS1B01G126000 chr1D 94.141 256 14 1 5 260 479502920 479503174 5.530000e-104 388
63 TraesCS1B01G126000 chr1D 89.888 178 17 1 3782 3959 202975833 202976009 1.280000e-55 228
64 TraesCS1B01G126000 chr1D 82.716 243 20 7 3738 3959 12258622 12258381 3.600000e-46 196
65 TraesCS1B01G126000 chr1D 96.667 60 2 0 3738 3797 202975768 202975827 2.900000e-17 100
66 TraesCS1B01G126000 chr3D 93.130 262 14 3 6 267 276433590 276433847 9.260000e-102 381
67 TraesCS1B01G126000 chr5A 92.549 255 18 1 4137 4391 487695344 487695091 9.320000e-97 364
68 TraesCS1B01G126000 chr6A 90.514 253 22 2 4142 4394 27353958 27354208 2.630000e-87 333
69 TraesCS1B01G126000 chr6A 90.551 254 21 2 4137 4389 530596646 530596897 2.630000e-87 333


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 TraesCS1B01G126000 chr1B 154147340 154151899 4559 False 8421.000000 8421 100.000000 1 4560 1 chr1B.!!$F1 4559
1 TraesCS1B01G126000 chr1B 55535652 55536583 931 True 1328.000000 1328 92.529000 5 931 1 chr1B.!!$R1 926
2 TraesCS1B01G126000 chr2A 195112236 195116626 4390 False 7908.000000 7908 99.180000 1 4390 1 chr2A.!!$F1 4389
3 TraesCS1B01G126000 chr2A 721734352 721738815 4463 False 2534.666667 4874 97.208333 1 4390 3 chr2A.!!$F3 4389
4 TraesCS1B01G126000 chr1A 14525007 14529380 4373 True 7740.000000 7740 98.545000 1 4393 1 chr1A.!!$R2 4392
5 TraesCS1B01G126000 chr1A 409841464 409842303 839 False 1068.000000 1068 89.675000 81 931 1 chr1A.!!$F1 850
6 TraesCS1B01G126000 chr7A 678167941 678172323 4382 True 7313.000000 7313 96.787000 1 4390 1 chr7A.!!$R1 4389
7 TraesCS1B01G126000 chr7D 509909321 509914521 5200 True 1721.500000 3157 94.047000 1 4122 4 chr7D.!!$R2 4121
8 TraesCS1B01G126000 chr5D 551015375 551020632 5257 True 1387.200000 3121 96.647400 1 4140 5 chr5D.!!$R3 4139
9 TraesCS1B01G126000 chr5D 254528652 254533815 5163 True 1351.600000 3149 96.184400 70 4122 5 chr5D.!!$R2 4052
10 TraesCS1B01G126000 chr4D 40830611 40835796 5185 False 1711.500000 3149 94.096250 1 4122 4 chr4D.!!$F5 4121
11 TraesCS1B01G126000 chrUn 315664133 315665063 930 True 1295.000000 1295 91.889000 5 931 1 chrUn.!!$R4 926
12 TraesCS1B01G126000 chrUn 260015016 260015956 940 True 1249.000000 1249 90.947000 5 931 1 chrUn.!!$R2 926
13 TraesCS1B01G126000 chrUn 262119216 262120156 940 True 1249.000000 1249 90.947000 5 931 1 chrUn.!!$R3 926
14 TraesCS1B01G126000 chr4A 409026420 409027337 917 True 1238.000000 1238 90.948000 5 931 1 chr4A.!!$R1 926
15 TraesCS1B01G126000 chr3A 568015272 568016118 846 True 1127.000000 1127 90.793000 84 931 1 chr3A.!!$R3 847
16 TraesCS1B01G126000 chr6D 39577318 39581230 3912 True 510.000000 935 95.697400 1443 3211 5 chr6D.!!$R3 1768

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
846 880 5.420739 TCTTTGGCTTCACTTTACAAACCTT 59.579 36.00 0.0 0.0 0.00 3.50 F
1050 2113 1.704641 TATCCGCACAGCCTCATACT 58.295 50.00 0.0 0.0 0.00 2.12 F
1919 3033 3.827876 TGATGGAAATTGAGCTTCAAGCA 59.172 39.13 13.1 0.0 45.56 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2372 5647 1.208706 TGGAGGCGATGGGTATTTCA 58.791 50.000 0.0 0.0 0.0 2.69 R
2385 5660 7.750229 TTCTAAATTATCATGTCATGGAGGC 57.250 36.000 12.9 0.0 0.0 4.70 R
3805 7411 8.487028 GTTCATCTCCCCTCTTTTCTCTATTTA 58.513 37.037 0.0 0.0 0.0 1.40 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
846 880 5.420739 TCTTTGGCTTCACTTTACAAACCTT 59.579 36.000 0.00 0.00 0.00 3.50
1050 2113 1.704641 TATCCGCACAGCCTCATACT 58.295 50.000 0.00 0.00 0.00 2.12
1919 3033 3.827876 TGATGGAAATTGAGCTTCAAGCA 59.172 39.130 13.10 0.00 45.56 3.91
2385 5660 6.207691 ACCAAAGATTTGAAATACCCATCG 57.792 37.500 6.87 0.00 40.55 3.84
3054 6588 9.851686 AGCATATTAGGAATGAAACATACAAGA 57.148 29.630 0.00 0.00 0.00 3.02
3805 7411 4.082845 TCTGATTCTCTCCGTCTTGAACT 58.917 43.478 0.00 0.00 0.00 3.01
4398 8113 8.725256 TCCATTAGGAGTAGAGATTGTAGTAGT 58.275 37.037 0.00 0.00 39.61 2.73
4399 8114 8.788806 CCATTAGGAGTAGAGATTGTAGTAGTG 58.211 40.741 0.00 0.00 36.89 2.74
4400 8115 9.344772 CATTAGGAGTAGAGATTGTAGTAGTGT 57.655 37.037 0.00 0.00 0.00 3.55
4401 8116 9.924010 ATTAGGAGTAGAGATTGTAGTAGTGTT 57.076 33.333 0.00 0.00 0.00 3.32
4402 8117 7.868906 AGGAGTAGAGATTGTAGTAGTGTTC 57.131 40.000 0.00 0.00 0.00 3.18
4403 8118 7.403671 AGGAGTAGAGATTGTAGTAGTGTTCA 58.596 38.462 0.00 0.00 0.00 3.18
4404 8119 7.889073 AGGAGTAGAGATTGTAGTAGTGTTCAA 59.111 37.037 0.00 0.00 0.00 2.69
4405 8120 8.521176 GGAGTAGAGATTGTAGTAGTGTTCAAA 58.479 37.037 0.00 0.00 0.00 2.69
4406 8121 9.909644 GAGTAGAGATTGTAGTAGTGTTCAAAA 57.090 33.333 0.00 0.00 0.00 2.44
4407 8122 9.694137 AGTAGAGATTGTAGTAGTGTTCAAAAC 57.306 33.333 0.00 0.00 0.00 2.43
4408 8123 9.694137 GTAGAGATTGTAGTAGTGTTCAAAACT 57.306 33.333 0.00 0.00 0.00 2.66
4409 8124 8.594881 AGAGATTGTAGTAGTGTTCAAAACTG 57.405 34.615 0.00 0.00 0.00 3.16
4410 8125 7.171678 AGAGATTGTAGTAGTGTTCAAAACTGC 59.828 37.037 0.00 0.00 0.00 4.40
4411 8126 6.765989 AGATTGTAGTAGTGTTCAAAACTGCA 59.234 34.615 0.00 0.00 33.21 4.41
4412 8127 6.935741 TTGTAGTAGTGTTCAAAACTGCAT 57.064 33.333 0.00 0.00 35.08 3.96
4413 8128 6.299023 TGTAGTAGTGTTCAAAACTGCATG 57.701 37.500 0.00 0.00 33.21 4.06
4414 8129 4.228912 AGTAGTGTTCAAAACTGCATGC 57.771 40.909 11.82 11.82 33.21 4.06
4415 8130 3.631686 AGTAGTGTTCAAAACTGCATGCA 59.368 39.130 21.29 21.29 33.21 3.96
4425 8140 2.558617 CTGCATGCAGGCACTAACA 58.441 52.632 35.39 0.00 39.25 2.41
4426 8141 0.169672 CTGCATGCAGGCACTAACAC 59.830 55.000 35.39 0.00 39.25 3.32
4427 8142 1.135315 GCATGCAGGCACTAACACG 59.865 57.895 20.11 0.00 36.02 4.49
4428 8143 1.577328 GCATGCAGGCACTAACACGT 61.577 55.000 20.11 0.00 36.02 4.49
4429 8144 0.874390 CATGCAGGCACTAACACGTT 59.126 50.000 0.00 0.00 36.02 3.99
4430 8145 1.135972 CATGCAGGCACTAACACGTTC 60.136 52.381 0.00 0.00 36.02 3.95
4431 8146 0.105964 TGCAGGCACTAACACGTTCT 59.894 50.000 0.00 0.00 36.02 3.01
4432 8147 0.790814 GCAGGCACTAACACGTTCTC 59.209 55.000 0.00 0.00 36.02 2.87
4433 8148 1.605712 GCAGGCACTAACACGTTCTCT 60.606 52.381 0.00 0.00 36.02 3.10
4434 8149 2.755650 CAGGCACTAACACGTTCTCTT 58.244 47.619 0.00 0.00 36.02 2.85
4435 8150 2.731976 CAGGCACTAACACGTTCTCTTC 59.268 50.000 0.00 0.00 36.02 2.87
4436 8151 2.628657 AGGCACTAACACGTTCTCTTCT 59.371 45.455 0.00 0.00 36.02 2.85
4437 8152 3.069729 AGGCACTAACACGTTCTCTTCTT 59.930 43.478 0.00 0.00 36.02 2.52
4438 8153 3.808174 GGCACTAACACGTTCTCTTCTTT 59.192 43.478 0.00 0.00 0.00 2.52
4439 8154 4.272748 GGCACTAACACGTTCTCTTCTTTT 59.727 41.667 0.00 0.00 0.00 2.27
4440 8155 5.198274 GCACTAACACGTTCTCTTCTTTTG 58.802 41.667 0.00 0.00 0.00 2.44
4441 8156 5.220605 GCACTAACACGTTCTCTTCTTTTGT 60.221 40.000 0.00 0.00 0.00 2.83
4442 8157 6.019318 GCACTAACACGTTCTCTTCTTTTGTA 60.019 38.462 0.00 0.00 0.00 2.41
4443 8158 7.556433 CACTAACACGTTCTCTTCTTTTGTAG 58.444 38.462 0.00 0.00 0.00 2.74
4444 8159 7.434307 CACTAACACGTTCTCTTCTTTTGTAGA 59.566 37.037 0.00 0.00 0.00 2.59
4445 8160 8.142551 ACTAACACGTTCTCTTCTTTTGTAGAT 58.857 33.333 0.00 0.00 31.54 1.98
4446 8161 9.622004 CTAACACGTTCTCTTCTTTTGTAGATA 57.378 33.333 0.00 0.00 31.54 1.98
4447 8162 8.882415 AACACGTTCTCTTCTTTTGTAGATAA 57.118 30.769 0.00 0.00 31.54 1.75
4448 8163 9.490379 AACACGTTCTCTTCTTTTGTAGATAAT 57.510 29.630 0.00 0.00 31.54 1.28
4465 8180 8.758829 TGTAGATAATAATAGGCATGTAGGTGG 58.241 37.037 0.00 0.00 0.00 4.61
4466 8181 8.978472 GTAGATAATAATAGGCATGTAGGTGGA 58.022 37.037 0.00 0.00 0.00 4.02
4467 8182 8.629821 AGATAATAATAGGCATGTAGGTGGAT 57.370 34.615 0.00 0.00 0.00 3.41
4468 8183 9.729550 AGATAATAATAGGCATGTAGGTGGATA 57.270 33.333 0.00 0.00 0.00 2.59
4472 8187 6.454223 AATAGGCATGTAGGTGGATAATGT 57.546 37.500 0.00 0.00 0.00 2.71
4473 8188 4.796110 AGGCATGTAGGTGGATAATGTT 57.204 40.909 0.00 0.00 0.00 2.71
4474 8189 5.129368 AGGCATGTAGGTGGATAATGTTT 57.871 39.130 0.00 0.00 0.00 2.83
4475 8190 6.260700 AGGCATGTAGGTGGATAATGTTTA 57.739 37.500 0.00 0.00 0.00 2.01
4476 8191 6.852404 AGGCATGTAGGTGGATAATGTTTAT 58.148 36.000 0.00 0.00 0.00 1.40
4477 8192 7.984475 AGGCATGTAGGTGGATAATGTTTATA 58.016 34.615 0.00 0.00 0.00 0.98
4478 8193 8.444783 AGGCATGTAGGTGGATAATGTTTATAA 58.555 33.333 0.00 0.00 0.00 0.98
4479 8194 8.512138 GGCATGTAGGTGGATAATGTTTATAAC 58.488 37.037 0.00 0.00 0.00 1.89
4480 8195 8.227791 GCATGTAGGTGGATAATGTTTATAACG 58.772 37.037 0.00 0.00 0.00 3.18
4481 8196 9.483916 CATGTAGGTGGATAATGTTTATAACGA 57.516 33.333 0.00 0.00 0.00 3.85
4482 8197 8.876275 TGTAGGTGGATAATGTTTATAACGAC 57.124 34.615 0.00 0.00 0.00 4.34
4483 8198 8.476447 TGTAGGTGGATAATGTTTATAACGACA 58.524 33.333 0.00 0.00 0.00 4.35
4484 8199 9.316730 GTAGGTGGATAATGTTTATAACGACAA 57.683 33.333 0.00 0.00 0.00 3.18
4485 8200 8.974060 AGGTGGATAATGTTTATAACGACAAT 57.026 30.769 0.00 0.00 0.00 2.71
4486 8201 9.052759 AGGTGGATAATGTTTATAACGACAATC 57.947 33.333 0.00 0.00 0.00 2.67
4487 8202 8.832521 GGTGGATAATGTTTATAACGACAATCA 58.167 33.333 0.00 0.00 0.00 2.57
4488 8203 9.646336 GTGGATAATGTTTATAACGACAATCAC 57.354 33.333 0.00 0.00 0.00 3.06
4489 8204 9.384764 TGGATAATGTTTATAACGACAATCACA 57.615 29.630 0.00 0.00 0.00 3.58
4493 8208 7.764695 ATGTTTATAACGACAATCACATCGA 57.235 32.000 0.00 0.00 40.86 3.59
4494 8209 7.583860 TGTTTATAACGACAATCACATCGAA 57.416 32.000 0.00 0.00 40.86 3.71
4495 8210 8.192068 TGTTTATAACGACAATCACATCGAAT 57.808 30.769 0.00 0.00 40.86 3.34
4496 8211 8.113675 TGTTTATAACGACAATCACATCGAATG 58.886 33.333 0.00 0.00 40.86 2.67
4497 8212 3.389687 AACGACAATCACATCGAATGC 57.610 42.857 0.00 0.00 40.86 3.56
4498 8213 1.665679 ACGACAATCACATCGAATGCC 59.334 47.619 0.00 0.00 40.86 4.40
4499 8214 1.935873 CGACAATCACATCGAATGCCT 59.064 47.619 0.00 0.00 40.86 4.75
4500 8215 2.286008 CGACAATCACATCGAATGCCTG 60.286 50.000 0.00 0.00 40.86 4.85
4501 8216 2.019249 ACAATCACATCGAATGCCTGG 58.981 47.619 0.00 0.00 0.00 4.45
4502 8217 2.291365 CAATCACATCGAATGCCTGGA 58.709 47.619 0.00 0.00 0.00 3.86
4503 8218 2.882761 CAATCACATCGAATGCCTGGAT 59.117 45.455 0.00 0.00 0.00 3.41
4504 8219 2.245159 TCACATCGAATGCCTGGATC 57.755 50.000 0.00 0.00 0.00 3.36
4505 8220 1.764723 TCACATCGAATGCCTGGATCT 59.235 47.619 0.00 0.00 0.00 2.75
4506 8221 1.871676 CACATCGAATGCCTGGATCTG 59.128 52.381 0.00 0.00 0.00 2.90
4507 8222 0.873054 CATCGAATGCCTGGATCTGC 59.127 55.000 0.00 0.00 0.00 4.26
4508 8223 0.471191 ATCGAATGCCTGGATCTGCA 59.529 50.000 0.00 7.40 42.52 4.41
4510 8225 0.873054 CGAATGCCTGGATCTGCATC 59.127 55.000 15.03 9.72 46.97 3.91
4511 8226 1.542767 CGAATGCCTGGATCTGCATCT 60.543 52.381 15.03 8.23 46.97 2.90
4512 8227 2.152830 GAATGCCTGGATCTGCATCTC 58.847 52.381 15.03 11.77 46.97 2.75
4513 8228 1.436326 ATGCCTGGATCTGCATCTCT 58.564 50.000 10.71 0.00 44.58 3.10
4514 8229 0.757512 TGCCTGGATCTGCATCTCTC 59.242 55.000 0.00 0.00 31.31 3.20
4515 8230 0.757512 GCCTGGATCTGCATCTCTCA 59.242 55.000 0.00 0.00 0.00 3.27
4516 8231 1.140452 GCCTGGATCTGCATCTCTCAA 59.860 52.381 0.00 0.00 0.00 3.02
4517 8232 2.421107 GCCTGGATCTGCATCTCTCAAA 60.421 50.000 0.00 0.00 0.00 2.69
4518 8233 3.748027 GCCTGGATCTGCATCTCTCAAAT 60.748 47.826 0.00 0.00 0.00 2.32
4519 8234 4.504514 GCCTGGATCTGCATCTCTCAAATA 60.505 45.833 0.00 0.00 0.00 1.40
4520 8235 5.803795 GCCTGGATCTGCATCTCTCAAATAT 60.804 44.000 0.00 0.00 0.00 1.28
4521 8236 6.239396 CCTGGATCTGCATCTCTCAAATATT 58.761 40.000 0.00 0.00 0.00 1.28
4522 8237 7.392418 CCTGGATCTGCATCTCTCAAATATTA 58.608 38.462 0.00 0.00 0.00 0.98
4523 8238 7.333921 CCTGGATCTGCATCTCTCAAATATTAC 59.666 40.741 0.00 0.00 0.00 1.89
4524 8239 7.971201 TGGATCTGCATCTCTCAAATATTACT 58.029 34.615 0.00 0.00 0.00 2.24
4525 8240 8.435187 TGGATCTGCATCTCTCAAATATTACTT 58.565 33.333 0.00 0.00 0.00 2.24
4526 8241 9.282569 GGATCTGCATCTCTCAAATATTACTTT 57.717 33.333 0.00 0.00 0.00 2.66
4528 8243 9.842775 ATCTGCATCTCTCAAATATTACTTTCA 57.157 29.630 0.00 0.00 0.00 2.69
4529 8244 9.671279 TCTGCATCTCTCAAATATTACTTTCAA 57.329 29.630 0.00 0.00 0.00 2.69
4530 8245 9.713740 CTGCATCTCTCAAATATTACTTTCAAC 57.286 33.333 0.00 0.00 0.00 3.18
4531 8246 9.453572 TGCATCTCTCAAATATTACTTTCAACT 57.546 29.630 0.00 0.00 0.00 3.16
4532 8247 9.928236 GCATCTCTCAAATATTACTTTCAACTC 57.072 33.333 0.00 0.00 0.00 3.01
4537 8252 9.886132 TCTCAAATATTACTTTCAACTCCTACC 57.114 33.333 0.00 0.00 0.00 3.18
4538 8253 8.712285 TCAAATATTACTTTCAACTCCTACCG 57.288 34.615 0.00 0.00 0.00 4.02
4539 8254 8.533657 TCAAATATTACTTTCAACTCCTACCGA 58.466 33.333 0.00 0.00 0.00 4.69
4540 8255 8.818057 CAAATATTACTTTCAACTCCTACCGAG 58.182 37.037 0.00 0.00 44.95 4.63
4541 8256 4.796038 TTACTTTCAACTCCTACCGAGG 57.204 45.455 0.00 0.00 43.57 4.63
4542 8257 1.900486 ACTTTCAACTCCTACCGAGGG 59.100 52.381 0.00 0.00 43.94 4.30
4543 8258 2.176889 CTTTCAACTCCTACCGAGGGA 58.823 52.381 0.00 0.00 43.94 4.20
4544 8259 1.553706 TTCAACTCCTACCGAGGGAC 58.446 55.000 0.00 0.00 43.94 4.46
4545 8260 0.324091 TCAACTCCTACCGAGGGACC 60.324 60.000 0.00 0.00 43.94 4.46
4546 8261 0.324460 CAACTCCTACCGAGGGACCT 60.324 60.000 0.00 0.00 43.94 3.85
4547 8262 0.412640 AACTCCTACCGAGGGACCTT 59.587 55.000 0.00 0.00 43.94 3.50
4548 8263 1.302907 ACTCCTACCGAGGGACCTTA 58.697 55.000 0.00 0.00 43.94 2.69
4549 8264 1.064091 ACTCCTACCGAGGGACCTTAC 60.064 57.143 0.00 0.00 43.94 2.34
4550 8265 0.259938 TCCTACCGAGGGACCTTACC 59.740 60.000 0.00 0.00 43.94 2.85
4551 8266 1.105759 CCTACCGAGGGACCTTACCG 61.106 65.000 0.00 0.00 39.48 4.02
4552 8267 1.076777 TACCGAGGGACCTTACCGG 60.077 63.158 13.55 13.55 45.09 5.28
4553 8268 1.570857 TACCGAGGGACCTTACCGGA 61.571 60.000 19.93 5.03 42.49 5.14
4554 8269 2.125961 CCGAGGGACCTTACCGGAG 61.126 68.421 9.46 0.00 42.49 4.63
4555 8270 1.077212 CGAGGGACCTTACCGGAGA 60.077 63.158 9.46 0.00 36.31 3.71
4556 8271 0.467659 CGAGGGACCTTACCGGAGAT 60.468 60.000 9.46 0.00 36.31 2.75
4557 8272 1.790818 GAGGGACCTTACCGGAGATT 58.209 55.000 9.46 0.00 36.31 2.40
4558 8273 2.750807 CGAGGGACCTTACCGGAGATTA 60.751 54.545 9.46 0.00 36.31 1.75
4559 8274 2.627221 GAGGGACCTTACCGGAGATTAC 59.373 54.545 9.46 0.00 36.31 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
846 880 7.310072 TGAAACTTGAACGAACACAATTCTA 57.690 32.000 0.00 0.00 0.00 2.10
1050 2113 6.214615 TGATGAGAATTACCCAAGTAGTCCAA 59.785 38.462 0.00 0.00 0.00 3.53
1446 2559 6.408770 AGATGAGGATAAAAGGGAAAAGGT 57.591 37.500 0.00 0.00 0.00 3.50
1919 3033 2.125512 GCCACGAAGGATGTCGCT 60.126 61.111 2.86 0.00 45.00 4.93
2372 5647 1.208706 TGGAGGCGATGGGTATTTCA 58.791 50.000 0.00 0.00 0.00 2.69
2385 5660 7.750229 TTCTAAATTATCATGTCATGGAGGC 57.250 36.000 12.90 0.00 0.00 4.70
3805 7411 8.487028 GTTCATCTCCCCTCTTTTCTCTATTTA 58.513 37.037 0.00 0.00 0.00 1.40
4107 7820 0.882474 CGACGACCCCTGGATCTATC 59.118 60.000 0.00 0.00 0.00 2.08
4393 8108 3.631686 TGCATGCAGTTTTGAACACTACT 59.368 39.130 18.46 0.00 0.00 2.57
4394 8109 3.963665 TGCATGCAGTTTTGAACACTAC 58.036 40.909 18.46 0.00 0.00 2.73
4395 8110 3.004629 CCTGCATGCAGTTTTGAACACTA 59.995 43.478 38.22 5.72 42.15 2.74
4396 8111 2.223876 CCTGCATGCAGTTTTGAACACT 60.224 45.455 38.22 0.00 42.15 3.55
4397 8112 2.129607 CCTGCATGCAGTTTTGAACAC 58.870 47.619 38.22 0.00 42.15 3.32
4398 8113 1.538634 GCCTGCATGCAGTTTTGAACA 60.539 47.619 38.22 6.89 42.15 3.18
4399 8114 1.142474 GCCTGCATGCAGTTTTGAAC 58.858 50.000 38.22 18.79 42.15 3.18
4400 8115 0.751452 TGCCTGCATGCAGTTTTGAA 59.249 45.000 38.22 20.39 42.15 2.69
4401 8116 0.032403 GTGCCTGCATGCAGTTTTGA 59.968 50.000 38.22 18.90 43.02 2.69
4402 8117 0.032952 AGTGCCTGCATGCAGTTTTG 59.967 50.000 38.22 26.65 42.11 2.44
4403 8118 1.619654 TAGTGCCTGCATGCAGTTTT 58.380 45.000 38.22 25.03 42.11 2.43
4404 8119 1.270550 GTTAGTGCCTGCATGCAGTTT 59.729 47.619 38.22 24.74 42.11 2.66
4405 8120 0.883833 GTTAGTGCCTGCATGCAGTT 59.116 50.000 38.22 25.04 42.11 3.16
4406 8121 0.250858 TGTTAGTGCCTGCATGCAGT 60.251 50.000 38.22 25.76 46.31 4.40
4407 8122 0.169672 GTGTTAGTGCCTGCATGCAG 59.830 55.000 35.88 35.88 43.02 4.41
4408 8123 1.576451 CGTGTTAGTGCCTGCATGCA 61.576 55.000 21.29 21.29 39.37 3.96
4409 8124 1.135315 CGTGTTAGTGCCTGCATGC 59.865 57.895 11.82 11.82 0.00 4.06
4410 8125 0.874390 AACGTGTTAGTGCCTGCATG 59.126 50.000 0.00 0.00 0.00 4.06
4411 8126 1.156736 GAACGTGTTAGTGCCTGCAT 58.843 50.000 0.00 0.00 0.00 3.96
4412 8127 0.105964 AGAACGTGTTAGTGCCTGCA 59.894 50.000 0.00 0.00 0.00 4.41
4413 8128 0.790814 GAGAACGTGTTAGTGCCTGC 59.209 55.000 0.00 0.00 0.00 4.85
4414 8129 2.440539 AGAGAACGTGTTAGTGCCTG 57.559 50.000 0.00 0.00 0.00 4.85
4415 8130 2.628657 AGAAGAGAACGTGTTAGTGCCT 59.371 45.455 0.00 0.00 0.00 4.75
4416 8131 3.027974 AGAAGAGAACGTGTTAGTGCC 57.972 47.619 0.00 0.00 0.00 5.01
4417 8132 5.198274 CAAAAGAAGAGAACGTGTTAGTGC 58.802 41.667 0.00 0.00 0.00 4.40
4418 8133 6.345920 ACAAAAGAAGAGAACGTGTTAGTG 57.654 37.500 0.00 0.00 0.00 2.74
4419 8134 7.486647 TCTACAAAAGAAGAGAACGTGTTAGT 58.513 34.615 0.00 0.00 0.00 2.24
4420 8135 7.925703 TCTACAAAAGAAGAGAACGTGTTAG 57.074 36.000 0.00 0.00 0.00 2.34
4421 8136 9.970395 TTATCTACAAAAGAAGAGAACGTGTTA 57.030 29.630 0.00 0.00 37.89 2.41
4422 8137 8.882415 TTATCTACAAAAGAAGAGAACGTGTT 57.118 30.769 0.00 0.00 37.89 3.32
4439 8154 8.758829 CCACCTACATGCCTATTATTATCTACA 58.241 37.037 0.00 0.00 0.00 2.74
4440 8155 8.978472 TCCACCTACATGCCTATTATTATCTAC 58.022 37.037 0.00 0.00 0.00 2.59
4441 8156 9.729550 ATCCACCTACATGCCTATTATTATCTA 57.270 33.333 0.00 0.00 0.00 1.98
4442 8157 8.629821 ATCCACCTACATGCCTATTATTATCT 57.370 34.615 0.00 0.00 0.00 1.98
4446 8161 8.614814 ACATTATCCACCTACATGCCTATTATT 58.385 33.333 0.00 0.00 0.00 1.40
4447 8162 8.162848 ACATTATCCACCTACATGCCTATTAT 57.837 34.615 0.00 0.00 0.00 1.28
4448 8163 7.568128 ACATTATCCACCTACATGCCTATTA 57.432 36.000 0.00 0.00 0.00 0.98
4449 8164 6.454223 ACATTATCCACCTACATGCCTATT 57.546 37.500 0.00 0.00 0.00 1.73
4450 8165 6.454223 AACATTATCCACCTACATGCCTAT 57.546 37.500 0.00 0.00 0.00 2.57
4451 8166 5.904984 AACATTATCCACCTACATGCCTA 57.095 39.130 0.00 0.00 0.00 3.93
4452 8167 4.796110 AACATTATCCACCTACATGCCT 57.204 40.909 0.00 0.00 0.00 4.75
4453 8168 8.512138 GTTATAAACATTATCCACCTACATGCC 58.488 37.037 0.00 0.00 0.00 4.40
4454 8169 8.227791 CGTTATAAACATTATCCACCTACATGC 58.772 37.037 0.00 0.00 0.00 4.06
4455 8170 9.483916 TCGTTATAAACATTATCCACCTACATG 57.516 33.333 0.00 0.00 0.00 3.21
4456 8171 9.485206 GTCGTTATAAACATTATCCACCTACAT 57.515 33.333 0.00 0.00 0.00 2.29
4457 8172 8.476447 TGTCGTTATAAACATTATCCACCTACA 58.524 33.333 0.00 0.00 0.00 2.74
4458 8173 8.876275 TGTCGTTATAAACATTATCCACCTAC 57.124 34.615 0.00 0.00 0.00 3.18
4460 8175 8.974060 ATTGTCGTTATAAACATTATCCACCT 57.026 30.769 0.00 0.00 0.00 4.00
4461 8176 8.832521 TGATTGTCGTTATAAACATTATCCACC 58.167 33.333 0.00 0.00 0.00 4.61
4462 8177 9.646336 GTGATTGTCGTTATAAACATTATCCAC 57.354 33.333 0.00 0.00 0.00 4.02
4463 8178 9.384764 TGTGATTGTCGTTATAAACATTATCCA 57.615 29.630 0.00 0.00 0.00 3.41
4467 8182 9.303537 TCGATGTGATTGTCGTTATAAACATTA 57.696 29.630 0.00 0.00 38.85 1.90
4468 8183 8.192068 TCGATGTGATTGTCGTTATAAACATT 57.808 30.769 0.00 0.00 38.85 2.71
4469 8184 7.764695 TCGATGTGATTGTCGTTATAAACAT 57.235 32.000 0.00 0.00 38.85 2.71
4470 8185 7.583860 TTCGATGTGATTGTCGTTATAAACA 57.416 32.000 0.00 0.00 38.85 2.83
4471 8186 7.110216 GCATTCGATGTGATTGTCGTTATAAAC 59.890 37.037 2.79 0.00 38.85 2.01
4472 8187 7.123190 GCATTCGATGTGATTGTCGTTATAAA 58.877 34.615 2.79 0.00 38.85 1.40
4473 8188 6.292649 GGCATTCGATGTGATTGTCGTTATAA 60.293 38.462 2.79 0.00 38.85 0.98
4474 8189 5.176774 GGCATTCGATGTGATTGTCGTTATA 59.823 40.000 2.79 0.00 38.85 0.98
4475 8190 4.024893 GGCATTCGATGTGATTGTCGTTAT 60.025 41.667 2.79 0.00 38.85 1.89
4476 8191 3.308595 GGCATTCGATGTGATTGTCGTTA 59.691 43.478 2.79 0.00 38.85 3.18
4477 8192 2.095853 GGCATTCGATGTGATTGTCGTT 59.904 45.455 2.79 0.00 38.85 3.85
4478 8193 1.665679 GGCATTCGATGTGATTGTCGT 59.334 47.619 2.79 0.00 38.85 4.34
4479 8194 1.935873 AGGCATTCGATGTGATTGTCG 59.064 47.619 2.79 0.00 37.58 4.35
4480 8195 2.032550 CCAGGCATTCGATGTGATTGTC 59.967 50.000 2.79 0.00 33.74 3.18
4481 8196 2.019249 CCAGGCATTCGATGTGATTGT 58.981 47.619 2.79 0.00 31.92 2.71
4482 8197 2.291365 TCCAGGCATTCGATGTGATTG 58.709 47.619 2.79 0.71 0.00 2.67
4483 8198 2.715749 TCCAGGCATTCGATGTGATT 57.284 45.000 2.79 0.00 0.00 2.57
4484 8199 2.371179 AGATCCAGGCATTCGATGTGAT 59.629 45.455 2.79 0.00 0.00 3.06
4485 8200 1.764723 AGATCCAGGCATTCGATGTGA 59.235 47.619 2.79 0.00 0.00 3.58
4486 8201 1.871676 CAGATCCAGGCATTCGATGTG 59.128 52.381 0.00 0.00 0.00 3.21
4487 8202 1.813092 GCAGATCCAGGCATTCGATGT 60.813 52.381 0.00 0.00 0.00 3.06
4488 8203 0.873054 GCAGATCCAGGCATTCGATG 59.127 55.000 0.00 0.00 0.00 3.84
4489 8204 0.471191 TGCAGATCCAGGCATTCGAT 59.529 50.000 0.60 0.00 34.58 3.59
4490 8205 1.906995 TGCAGATCCAGGCATTCGA 59.093 52.632 0.60 0.00 34.58 3.71
4491 8206 4.545929 TGCAGATCCAGGCATTCG 57.454 55.556 0.60 0.00 34.58 3.34
4495 8210 0.757512 GAGAGATGCAGATCCAGGCA 59.242 55.000 6.75 6.75 45.23 4.75
4496 8211 0.757512 TGAGAGATGCAGATCCAGGC 59.242 55.000 0.00 0.00 0.00 4.85
4497 8212 3.555527 TTTGAGAGATGCAGATCCAGG 57.444 47.619 0.00 0.00 0.00 4.45
4498 8213 8.095792 AGTAATATTTGAGAGATGCAGATCCAG 58.904 37.037 0.00 0.00 0.00 3.86
4499 8214 7.971201 AGTAATATTTGAGAGATGCAGATCCA 58.029 34.615 0.00 0.00 0.00 3.41
4500 8215 8.845413 AAGTAATATTTGAGAGATGCAGATCC 57.155 34.615 0.00 0.00 0.00 3.36
4502 8217 9.842775 TGAAAGTAATATTTGAGAGATGCAGAT 57.157 29.630 0.00 0.00 0.00 2.90
4503 8218 9.671279 TTGAAAGTAATATTTGAGAGATGCAGA 57.329 29.630 0.00 0.00 0.00 4.26
4504 8219 9.713740 GTTGAAAGTAATATTTGAGAGATGCAG 57.286 33.333 0.00 0.00 0.00 4.41
4505 8220 9.453572 AGTTGAAAGTAATATTTGAGAGATGCA 57.546 29.630 0.00 0.00 0.00 3.96
4506 8221 9.928236 GAGTTGAAAGTAATATTTGAGAGATGC 57.072 33.333 0.00 0.00 0.00 3.91
4511 8226 9.886132 GGTAGGAGTTGAAAGTAATATTTGAGA 57.114 33.333 0.00 0.00 0.00 3.27
4512 8227 8.818057 CGGTAGGAGTTGAAAGTAATATTTGAG 58.182 37.037 0.00 0.00 0.00 3.02
4513 8228 8.533657 TCGGTAGGAGTTGAAAGTAATATTTGA 58.466 33.333 0.00 0.00 0.00 2.69
4514 8229 8.712285 TCGGTAGGAGTTGAAAGTAATATTTG 57.288 34.615 0.00 0.00 0.00 2.32
4515 8230 8.943909 CTCGGTAGGAGTTGAAAGTAATATTT 57.056 34.615 0.00 0.00 38.02 1.40
4532 8247 1.105759 CGGTAAGGTCCCTCGGTAGG 61.106 65.000 0.00 0.00 43.25 3.18
4533 8248 1.105759 CCGGTAAGGTCCCTCGGTAG 61.106 65.000 0.00 0.00 36.38 3.18
4534 8249 1.076777 CCGGTAAGGTCCCTCGGTA 60.077 63.158 0.00 0.00 36.38 4.02
4535 8250 2.363406 CCGGTAAGGTCCCTCGGT 60.363 66.667 0.00 0.00 36.38 4.69
4536 8251 2.043652 TCCGGTAAGGTCCCTCGG 60.044 66.667 0.00 5.77 41.99 4.63
4537 8252 0.467659 ATCTCCGGTAAGGTCCCTCG 60.468 60.000 0.00 0.00 41.99 4.63
4538 8253 1.790818 AATCTCCGGTAAGGTCCCTC 58.209 55.000 0.00 0.00 41.99 4.30
4539 8254 2.675583 GTAATCTCCGGTAAGGTCCCT 58.324 52.381 0.00 0.00 41.99 4.20


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

AutoCloner maintained by Alex Coulton.