Multiple sequence alignment - TraesCS7B01G199500

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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 TraesCS7B01G199500 chr7B 100.000 7973 0 0 1 7973 358881445 358873473 0.000000e+00 14724
1 TraesCS7B01G199500 chr7B 87.609 460 52 2 7519 7973 313311418 313310959 5.480000e-146 529
2 TraesCS7B01G199500 chr7B 96.748 123 4 0 3079 3201 358878238 358878116 1.050000e-48 206
3 TraesCS7B01G199500 chr7B 96.748 123 4 0 3208 3330 358878367 358878245 1.050000e-48 206
4 TraesCS7B01G199500 chr7B 83.721 172 10 5 7237 7400 358874103 358873942 6.450000e-31 147
5 TraesCS7B01G199500 chr7B 83.721 172 10 5 7343 7504 358874209 358874046 6.450000e-31 147
6 TraesCS7B01G199500 chr7B 90.196 102 5 2 7197 7293 358874043 358873942 2.340000e-25 128
7 TraesCS7B01G199500 chr7B 90.196 102 5 2 7403 7504 358874249 358874153 2.340000e-25 128
8 TraesCS7B01G199500 chr7D 96.349 4136 97 26 3860 7973 293213240 293217343 0.000000e+00 6752
9 TraesCS7B01G199500 chr7D 96.838 2530 38 12 1344 3853 293210756 293213263 0.000000e+00 4191
10 TraesCS7B01G199500 chr7D 92.046 1295 64 14 1 1284 293209147 293210413 0.000000e+00 1784
11 TraesCS7B01G199500 chr7D 87.419 461 53 2 7518 7973 337237128 337237588 7.090000e-145 525
12 TraesCS7B01G199500 chr7D 87.419 461 53 2 7518 7973 337271325 337271785 7.090000e-145 525
13 TraesCS7B01G199500 chr7D 83.289 377 58 4 1 373 365550262 365550637 7.660000e-90 342
14 TraesCS7B01G199500 chr7D 95.070 142 6 1 3208 3348 293212473 293212614 1.040000e-53 222
15 TraesCS7B01G199500 chr7D 97.674 129 2 1 3078 3206 293212618 293212745 3.750000e-53 220
16 TraesCS7B01G199500 chr7D 85.116 215 12 6 7310 7504 293216563 293216777 1.360000e-47 202
17 TraesCS7B01G199500 chr7D 83.408 223 15 8 7190 7400 293216669 293216881 3.800000e-43 187
18 TraesCS7B01G199500 chr7D 93.103 116 7 1 7403 7517 293216559 293216674 1.380000e-37 169
19 TraesCS7B01G199500 chr7A 97.192 3454 72 14 3860 7304 339519660 339523097 0.000000e+00 5818
20 TraesCS7B01G199500 chr7A 96.050 2582 49 10 870 3431 339514792 339517340 0.000000e+00 4154
21 TraesCS7B01G199500 chr7A 91.657 875 61 9 1 870 339507256 339508123 0.000000e+00 1201
22 TraesCS7B01G199500 chr7A 91.899 716 42 6 7267 7973 339523098 339523806 0.000000e+00 987
23 TraesCS7B01G199500 chr7A 98.587 283 4 0 3428 3710 339518158 339518440 1.190000e-137 501
24 TraesCS7B01G199500 chr7A 96.689 151 5 0 3703 3853 339519533 339519683 1.330000e-62 252
25 TraesCS7B01G199500 chr7A 95.775 142 5 1 3208 3348 339516970 339517111 2.240000e-55 228
26 TraesCS7B01G199500 chr7A 96.269 134 5 0 870 1003 339508427 339508560 3.750000e-53 220
27 TraesCS7B01G199500 chr7A 96.899 129 4 0 3078 3206 339517115 339517243 4.850000e-52 217
28 TraesCS7B01G199500 chr7A 81.250 224 19 6 7190 7400 339523130 339523343 8.280000e-35 159
29 TraesCS7B01G199500 chr7A 94.118 102 6 0 7403 7504 339522985 339523086 1.070000e-33 156
30 TraesCS7B01G199500 chr7A 94.898 98 5 0 7407 7504 339523141 339523238 3.850000e-33 154
31 TraesCS7B01G199500 chr7A 86.139 101 8 2 7199 7293 339523243 339523343 3.940000e-18 104
32 TraesCS7B01G199500 chr6D 87.419 461 53 2 7518 7973 224008537 224008077 7.090000e-145 525
33 TraesCS7B01G199500 chr5D 87.419 461 53 2 7518 7973 123030121 123029661 7.090000e-145 525
34 TraesCS7B01G199500 chr6B 87.391 460 53 2 7519 7973 367294021 367294480 2.550000e-144 523
35 TraesCS7B01G199500 chr4B 87.391 460 53 2 7519 7973 314020782 314020323 2.550000e-144 523
36 TraesCS7B01G199500 chr4B 83.551 383 54 9 1 377 441685100 441684721 4.580000e-92 350
37 TraesCS7B01G199500 chr2D 84.115 384 51 9 1 378 430655509 430655130 5.880000e-96 363
38 TraesCS7B01G199500 chr3B 83.684 380 54 8 3 377 434034054 434033678 1.270000e-92 351
39 TraesCS7B01G199500 chr4A 83.508 382 50 7 1 377 106895765 106896138 2.130000e-90 344
40 TraesCS7B01G199500 chr4A 82.723 382 59 7 1 377 73586723 73587102 4.610000e-87 333
41 TraesCS7B01G199500 chr2B 82.245 383 54 13 1 377 495719199 495718825 1.290000e-82 318
42 TraesCS7B01G199500 chr2A 80.870 345 52 13 429 763 703658631 703658291 7.940000e-65 259
43 TraesCS7B01G199500 chr5A 80.923 325 48 13 429 742 529910095 529909774 2.220000e-60 244
44 TraesCS7B01G199500 chr1D 81.863 204 27 10 495 689 282138825 282138623 6.400000e-36 163


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 TraesCS7B01G199500 chr7B 358873473 358881445 7972 True 14724.000000 14724 100.000000 1 7973 1 chr7B.!!$R2 7972
1 TraesCS7B01G199500 chr7D 293209147 293217343 8196 False 1715.875000 6752 92.450500 1 7973 8 chr7D.!!$F4 7972
2 TraesCS7B01G199500 chr7A 339514792 339523806 9014 False 1157.272727 5818 93.590545 870 7973 11 chr7A.!!$F2 7103
3 TraesCS7B01G199500 chr7A 339507256 339508560 1304 False 710.500000 1201 93.963000 1 1003 2 chr7A.!!$F1 1002

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
388 395 0.038892 ACGTATCACCGCGACAGTTT 60.039 50.000 8.23 0.0 0.00 2.66 F
1042 1358 0.250684 TGCGTCAACCCACACATCAT 60.251 50.000 0.00 0.0 0.00 2.45 F
1043 1359 0.447801 GCGTCAACCCACACATCATC 59.552 55.000 0.00 0.0 0.00 2.92 F
2604 3206 1.066002 CTCCTGTTGGTGTTGTGCAAG 59.934 52.381 0.00 0.0 34.23 4.01 F
3521 4963 2.507407 TGAGGGCCCACAAATTCTAC 57.493 50.000 27.56 2.3 0.00 2.59 F
3806 6348 3.196685 TCTTGGTTGTTTGGTGGGAAAAG 59.803 43.478 0.00 0.0 0.00 2.27 F
5078 7625 2.930682 GGATTCGAGGAAAAGAAGACGG 59.069 50.000 0.00 0.0 0.00 4.79 F
5268 7815 1.281867 TGGAGGTTGATGGTGATGACC 59.718 52.381 0.00 0.0 43.48 4.02 F
6957 9504 1.263217 CGTGTTTACAGTGTGCCCTTC 59.737 52.381 5.88 0.0 0.00 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1254 1571 0.616395 TAGGGCTTGACATCGTGGGA 60.616 55.000 0.00 0.0 0.00 4.37 R
2604 3206 0.031994 ATTGTTGCTGGCCGTTGAAC 59.968 50.000 0.00 0.0 0.00 3.18 R
3039 3641 0.810648 TTGCCCATCAACGCTCAATC 59.189 50.000 0.00 0.0 0.00 2.67 R
3950 6492 1.218875 TTGAACACGGCACTAGCACG 61.219 55.000 0.00 0.0 44.61 5.34 R
5078 7625 1.071605 CAAGTGCGTTACTGCTCCTC 58.928 55.000 0.00 0.0 40.26 3.71 R
5268 7815 1.372087 GGTGCATCTGCTTCCTTCCG 61.372 60.000 3.53 0.0 42.66 4.30 R
6628 9175 0.721718 CAGCCTCGACGTCCAAAATC 59.278 55.000 10.58 0.0 0.00 2.17 R
6961 9508 3.699038 TCACCTGTTGGAACTTGGAAAAG 59.301 43.478 8.44 0.0 37.04 2.27 R
7917 10518 2.706339 AGCTAACTGGAATGCAGAGG 57.294 50.000 9.20 0.0 0.00 3.69 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
96 98 0.763223 AGACGGAGGTTTGTGGGACT 60.763 55.000 0.00 0.00 0.00 3.85
99 101 0.602905 CGGAGGTTTGTGGGACTCAC 60.603 60.000 0.00 0.00 46.23 3.51
107 109 1.080434 GTGGGACTCACGAGCTCAC 60.080 63.158 15.40 0.00 36.56 3.51
154 157 3.687321 CTCATGGCTCCGTGGTGGG 62.687 68.421 8.16 0.00 38.76 4.61
173 177 1.248486 GCCCCTCCAACAGAGTTTTC 58.752 55.000 0.00 0.00 41.47 2.29
234 238 5.397142 AAATTTCAGCCCAATCTGAGAAC 57.603 39.130 0.00 0.00 43.23 3.01
253 257 8.633075 TGAGAACTTTTATTTCTGCACAAAAG 57.367 30.769 0.00 0.00 41.54 2.27
263 267 4.829064 TCTGCACAAAAGTAACACCATC 57.171 40.909 0.00 0.00 0.00 3.51
305 309 3.367025 CGTCAGTCGGGTTAGTTTCATTC 59.633 47.826 0.00 0.00 35.71 2.67
336 340 7.106439 TGCAAATTAGAGTCCAAAACAAGAA 57.894 32.000 0.00 0.00 0.00 2.52
362 366 5.606348 AATTGTTTGGAAAAGTGGCTACA 57.394 34.783 2.02 0.00 0.00 2.74
382 389 1.093972 TTTAGGACGTATCACCGCGA 58.906 50.000 8.23 0.00 0.00 5.87
388 395 0.038892 ACGTATCACCGCGACAGTTT 60.039 50.000 8.23 0.00 0.00 2.66
425 432 1.847798 TACTGCCGGCAATCACCCTT 61.848 55.000 32.09 9.40 0.00 3.95
464 471 6.670077 AGTTCAGAGAAAACTGACAACTTC 57.330 37.500 0.00 0.00 44.94 3.01
475 482 2.227388 CTGACAACTTCCAACATCAGCC 59.773 50.000 0.00 0.00 0.00 4.85
488 495 1.133884 CATCAGCCCATCCAGTCATGT 60.134 52.381 0.00 0.00 0.00 3.21
489 496 0.253894 TCAGCCCATCCAGTCATGTG 59.746 55.000 0.00 0.00 0.00 3.21
511 518 2.121948 AGGCTGGATCATAGCTTCACA 58.878 47.619 17.41 0.00 40.92 3.58
516 523 4.743045 GCTGGATCATAGCTTCACACAGAT 60.743 45.833 12.46 0.00 38.14 2.90
527 534 5.091431 GCTTCACACAGATAAACATCAAGC 58.909 41.667 0.00 0.00 0.00 4.01
562 569 3.573967 TGCTCCTCATGCAGAATACGATA 59.426 43.478 0.00 0.00 35.31 2.92
601 608 3.767816 CACATGGGTGCAAGCACT 58.232 55.556 22.79 2.47 45.52 4.40
635 642 1.137825 GAGAACGAGAGACCAGCGG 59.862 63.158 0.00 0.00 0.00 5.52
744 753 1.003233 GCCTTGGATATCGCCTCCC 60.003 63.158 0.00 0.00 31.32 4.30
783 792 5.278266 GCTTTGCCTGACTTGTAAACATACA 60.278 40.000 0.00 0.00 0.00 2.29
1042 1358 0.250684 TGCGTCAACCCACACATCAT 60.251 50.000 0.00 0.00 0.00 2.45
1043 1359 0.447801 GCGTCAACCCACACATCATC 59.552 55.000 0.00 0.00 0.00 2.92
1044 1360 1.807139 CGTCAACCCACACATCATCA 58.193 50.000 0.00 0.00 0.00 3.07
1089 1406 4.506255 CGAGCCCCATCAACCCCC 62.506 72.222 0.00 0.00 0.00 5.40
1254 1571 1.386772 TAATCCCCCGGCCTCCAAT 60.387 57.895 0.00 0.00 0.00 3.16
1286 1603 1.997311 GCCCTAACCCTAACCCCGT 60.997 63.158 0.00 0.00 0.00 5.28
1287 1604 1.976132 GCCCTAACCCTAACCCCGTC 61.976 65.000 0.00 0.00 0.00 4.79
1288 1605 1.340399 CCCTAACCCTAACCCCGTCC 61.340 65.000 0.00 0.00 0.00 4.79
1289 1606 1.340399 CCTAACCCTAACCCCGTCCC 61.340 65.000 0.00 0.00 0.00 4.46
1290 1607 1.306911 TAACCCTAACCCCGTCCCC 60.307 63.158 0.00 0.00 0.00 4.81
1564 2164 2.499685 GGTCCCGTTCTCCATCCG 59.500 66.667 0.00 0.00 0.00 4.18
2040 2642 8.475639 GGTTTCTGTATGTACTTAGATCCTTCA 58.524 37.037 0.00 0.00 0.00 3.02
2271 2873 3.965347 AGTACGTTATCCTGCCTAATGGT 59.035 43.478 0.00 0.00 35.27 3.55
2485 3087 7.148557 GCTCTGTTTTCTGGACTGTTACTAATC 60.149 40.741 0.00 0.00 0.00 1.75
2546 3148 3.244078 TGCATCGTTATCCTGGACCATAC 60.244 47.826 0.00 0.00 0.00 2.39
2604 3206 1.066002 CTCCTGTTGGTGTTGTGCAAG 59.934 52.381 0.00 0.00 34.23 4.01
3039 3641 2.551270 GACGCGGTTGCTGAACAG 59.449 61.111 12.47 0.00 39.65 3.16
3296 3916 3.838244 TTCGGAATGATAAGGACCTGG 57.162 47.619 0.00 0.00 0.00 4.45
3330 3950 7.798596 AATAATAGGACATCAGTTGCTTCTG 57.201 36.000 3.04 3.04 36.85 3.02
3521 4963 2.507407 TGAGGGCCCACAAATTCTAC 57.493 50.000 27.56 2.30 0.00 2.59
3557 4999 3.906720 TCTTATGTACTGGAACCCTGC 57.093 47.619 0.00 0.00 0.00 4.85
3598 5040 7.486407 AATACTTTCCTTTTGCTTCCATGAT 57.514 32.000 0.00 0.00 0.00 2.45
3800 6342 7.800155 ATTAAATTTCTTGGTTGTTTGGTGG 57.200 32.000 0.00 0.00 0.00 4.61
3806 6348 3.196685 TCTTGGTTGTTTGGTGGGAAAAG 59.803 43.478 0.00 0.00 0.00 2.27
3847 6389 6.061441 TCTTGTGTACCATTGTTCAGTCATT 58.939 36.000 0.00 0.00 0.00 2.57
3848 6390 5.687770 TGTGTACCATTGTTCAGTCATTG 57.312 39.130 0.00 0.00 0.00 2.82
3849 6391 5.372373 TGTGTACCATTGTTCAGTCATTGA 58.628 37.500 0.00 0.00 0.00 2.57
3850 6392 5.825151 TGTGTACCATTGTTCAGTCATTGAA 59.175 36.000 0.00 0.00 43.40 2.69
3851 6393 6.489700 TGTGTACCATTGTTCAGTCATTGAAT 59.510 34.615 0.00 0.00 46.85 2.57
3852 6394 7.014134 TGTGTACCATTGTTCAGTCATTGAATT 59.986 33.333 0.00 0.00 46.85 2.17
3853 6395 7.538678 GTGTACCATTGTTCAGTCATTGAATTC 59.461 37.037 0.00 0.00 46.85 2.17
3854 6396 6.653526 ACCATTGTTCAGTCATTGAATTCA 57.346 33.333 3.38 3.38 46.85 2.57
3855 6397 7.053316 ACCATTGTTCAGTCATTGAATTCAA 57.947 32.000 22.52 22.52 46.85 2.69
3856 6398 7.149973 ACCATTGTTCAGTCATTGAATTCAAG 58.850 34.615 24.17 16.29 46.85 3.02
3857 6399 7.149973 CCATTGTTCAGTCATTGAATTCAAGT 58.850 34.615 24.17 11.17 46.85 3.16
3858 6400 7.115805 CCATTGTTCAGTCATTGAATTCAAGTG 59.884 37.037 24.17 20.28 46.85 3.16
3859 6401 6.075762 TGTTCAGTCATTGAATTCAAGTGG 57.924 37.500 24.17 16.31 46.85 4.00
3860 6402 5.593909 TGTTCAGTCATTGAATTCAAGTGGT 59.406 36.000 24.17 6.61 46.85 4.16
3861 6403 6.770303 TGTTCAGTCATTGAATTCAAGTGGTA 59.230 34.615 24.17 2.38 46.85 3.25
3862 6404 6.801539 TCAGTCATTGAATTCAAGTGGTAC 57.198 37.500 24.17 16.38 39.47 3.34
3863 6405 5.705441 TCAGTCATTGAATTCAAGTGGTACC 59.295 40.000 24.17 4.43 39.47 3.34
3864 6406 5.473162 CAGTCATTGAATTCAAGTGGTACCA 59.527 40.000 24.17 11.60 39.47 3.25
3865 6407 6.151648 CAGTCATTGAATTCAAGTGGTACCAT 59.848 38.462 24.17 0.00 39.47 3.55
3866 6408 6.721208 AGTCATTGAATTCAAGTGGTACCATT 59.279 34.615 24.17 11.73 39.47 3.16
3867 6409 6.808212 GTCATTGAATTCAAGTGGTACCATTG 59.192 38.462 24.17 20.94 39.47 2.82
3868 6410 6.493115 TCATTGAATTCAAGTGGTACCATTGT 59.507 34.615 24.17 2.95 39.47 2.71
3869 6411 6.723298 TTGAATTCAAGTGGTACCATTGTT 57.277 33.333 19.72 13.38 0.00 2.83
3870 6412 6.325919 TGAATTCAAGTGGTACCATTGTTC 57.674 37.500 19.72 19.72 0.00 3.18
3871 6413 5.830457 TGAATTCAAGTGGTACCATTGTTCA 59.170 36.000 19.72 21.51 0.00 3.18
3872 6414 5.964958 ATTCAAGTGGTACCATTGTTCAG 57.035 39.130 19.72 4.62 0.00 3.02
3873 6415 4.431416 TCAAGTGGTACCATTGTTCAGT 57.569 40.909 19.72 0.00 0.00 3.41
3874 6416 4.385825 TCAAGTGGTACCATTGTTCAGTC 58.614 43.478 19.72 1.13 0.00 3.51
3875 6417 4.133820 CAAGTGGTACCATTGTTCAGTCA 58.866 43.478 19.72 0.00 0.00 3.41
3876 6418 4.640771 AGTGGTACCATTGTTCAGTCAT 57.359 40.909 19.72 0.00 0.00 3.06
3950 6492 8.455682 TCCATTCGATTGTTACAGTTTATTTCC 58.544 33.333 6.56 0.00 0.00 3.13
4027 6570 8.638685 CAAGGATTGCTTAAGGAATATGTTTG 57.361 34.615 20.65 16.84 40.39 2.93
4048 6591 5.155278 TGCTTTGAAAATCCTGCATGATT 57.845 34.783 11.02 11.02 36.53 2.57
4116 6663 7.437748 CCCAATTGACATGGTTACACTTTTTA 58.562 34.615 7.12 0.00 36.14 1.52
4649 7196 9.881773 AATGACTGGTATGGAATAATGGTAATT 57.118 29.630 0.00 0.00 0.00 1.40
4886 7433 6.538209 AGAGTCAGGAGGGATAGAGATAAA 57.462 41.667 0.00 0.00 0.00 1.40
5078 7625 2.930682 GGATTCGAGGAAAAGAAGACGG 59.069 50.000 0.00 0.00 0.00 4.79
5268 7815 1.281867 TGGAGGTTGATGGTGATGACC 59.718 52.381 0.00 0.00 43.48 4.02
5694 8241 4.770795 CGGATTCTTATTCTGACCAACCT 58.229 43.478 0.00 0.00 0.00 3.50
5881 8428 3.739810 AGAAATGATGCATGATCGAGACG 59.260 43.478 2.46 0.00 33.17 4.18
6135 8682 4.963318 TCTTTGATGTTCTGTGAGGTCT 57.037 40.909 0.00 0.00 0.00 3.85
6136 8683 5.296151 TCTTTGATGTTCTGTGAGGTCTT 57.704 39.130 0.00 0.00 0.00 3.01
6137 8684 5.300752 TCTTTGATGTTCTGTGAGGTCTTC 58.699 41.667 0.00 0.00 0.00 2.87
6165 8712 5.626142 TGGAAGCAGTTTAGGTATGTTTGA 58.374 37.500 0.00 0.00 0.00 2.69
6188 8735 6.583050 TGACAGTGGTTACAAAAAGAAAAACG 59.417 34.615 0.00 0.00 0.00 3.60
6218 8765 4.331968 TGTAGTGCTCCTTAAACCATTGG 58.668 43.478 0.00 0.00 0.00 3.16
6231 8778 8.213679 CCTTAAACCATTGGAGATCTGAAGATA 58.786 37.037 10.37 0.00 34.37 1.98
6258 8805 5.914898 TTTCCTGAACAGATACGAGATCA 57.085 39.130 3.19 0.00 0.00 2.92
6268 8815 6.873997 ACAGATACGAGATCAACCACATAAA 58.126 36.000 0.00 0.00 0.00 1.40
6347 8894 8.741841 TGCATAATTCACAATTTGATCTGAGAA 58.258 29.630 2.79 0.00 32.84 2.87
6529 9076 6.039829 GGCCTTGGATCTCGAAAAAGATAATT 59.960 38.462 0.00 0.00 36.13 1.40
6623 9170 2.435805 TCGAAAATGCTGGAGCTCCTAT 59.564 45.455 32.28 20.44 42.66 2.57
6624 9171 2.805099 CGAAAATGCTGGAGCTCCTATC 59.195 50.000 32.28 20.55 42.66 2.08
6628 9175 1.284408 GCTGGAGCTCCTATCGTCG 59.716 63.158 32.28 13.00 38.21 5.12
6732 9279 5.778542 ACTATCAGTAAGAGGGAAGGCTTA 58.221 41.667 0.00 0.00 0.00 3.09
6832 9379 4.756084 AGACAGCTGCTGTAAACATTTC 57.244 40.909 33.04 18.56 45.44 2.17
6926 9473 9.745880 GATGCTCAATATTTGATCTGAAATTGT 57.254 29.630 0.00 0.00 39.30 2.71
6957 9504 1.263217 CGTGTTTACAGTGTGCCCTTC 59.737 52.381 5.88 0.00 0.00 3.46
6961 9508 4.392138 GTGTTTACAGTGTGCCCTTCTATC 59.608 45.833 5.88 0.00 0.00 2.08
6962 9509 4.286032 TGTTTACAGTGTGCCCTTCTATCT 59.714 41.667 5.88 0.00 0.00 1.98
7060 9607 7.041644 CCAACTTGATTTTCTTTGCACATGATT 60.042 33.333 0.00 0.00 0.00 2.57
7091 9638 6.106877 TGAAAGTTTTCACGAGACTTTGAG 57.893 37.500 12.51 0.00 42.03 3.02
7120 9667 8.358148 TGTACTTGTTTTACTTCAACAAAACCA 58.642 29.630 7.29 0.00 42.23 3.67
7295 9848 7.658525 AATGAAGCCACCACATTGAATATAA 57.341 32.000 0.00 0.00 33.79 0.98
7328 9919 7.884816 TTGTGTAAGAAATCTAACTTCTCCG 57.115 36.000 0.00 0.00 31.85 4.63
7336 9927 2.376109 TCTAACTTCTCCGCCTAGTGG 58.624 52.381 0.00 0.00 33.99 4.00
7393 9991 4.211125 TGAGTAAAATGAAGCCACCACAA 58.789 39.130 0.00 0.00 0.00 3.33
7563 10163 7.994425 TCATATGCTCTTGTTTGGACTTTAA 57.006 32.000 0.00 0.00 0.00 1.52
7574 10174 8.527567 TTGTTTGGACTTTAAAAACTTGACAG 57.472 30.769 0.00 0.00 35.35 3.51
7611 10211 7.009540 GGCCTAAAGAATTTGTCATTTTGATCG 59.990 37.037 0.00 0.00 39.63 3.69
7612 10212 7.463251 GCCTAAAGAATTTGTCATTTTGATCGC 60.463 37.037 0.00 0.00 39.63 4.58
7662 10263 4.640201 AGCAAAACTGAACTGTACACATGT 59.360 37.500 0.00 0.00 0.00 3.21
7666 10267 7.647715 GCAAAACTGAACTGTACACATGTTAAT 59.352 33.333 0.00 0.00 0.00 1.40
7693 10294 7.160726 GGGTTGAATTCATTGAGATTTTTCCA 58.839 34.615 9.40 0.00 0.00 3.53
7759 10360 7.454260 TGATGCATGTCTCGTCTATATACTT 57.546 36.000 2.46 0.00 0.00 2.24
7843 10444 7.035004 GCATGGTACTGAATTTAAAGATGCAA 58.965 34.615 0.00 0.00 34.10 4.08
7896 10497 7.174080 TGGAACAAGTTCGTCATTAATGATTGA 59.826 33.333 25.01 20.49 40.37 2.57
7917 10518 3.408288 TTTGTGTTCCGTGCTAACAAC 57.592 42.857 0.00 0.00 38.50 3.32
7918 10519 1.301423 TGTGTTCCGTGCTAACAACC 58.699 50.000 0.00 0.00 38.50 3.77
7919 10520 1.134340 TGTGTTCCGTGCTAACAACCT 60.134 47.619 0.00 0.00 38.50 3.50
7931 10532 2.664402 AACAACCTCTGCATTCCAGT 57.336 45.000 0.00 0.00 42.38 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 63 1.002087 CGTCTGCCCTAACTCCAACTT 59.998 52.381 0.00 0.00 0.00 2.66
154 157 1.248486 GAAAACTCTGTTGGAGGGGC 58.752 55.000 0.00 0.00 45.83 5.80
163 166 6.744112 TGAAAATTATTGGCGAAAACTCTGT 58.256 32.000 0.00 0.00 0.00 3.41
195 199 9.659830 GCTGAAATTTTACGAAGACTTTTTCTA 57.340 29.630 0.00 0.00 32.51 2.10
203 207 4.759516 TGGGCTGAAATTTTACGAAGAC 57.240 40.909 0.00 0.00 0.00 3.01
207 211 5.007034 TCAGATTGGGCTGAAATTTTACGA 58.993 37.500 0.00 0.00 41.65 3.43
234 238 8.539674 GGTGTTACTTTTGTGCAGAAATAAAAG 58.460 33.333 10.13 12.49 42.69 2.27
253 257 5.637104 CAGCATAACTACGATGGTGTTAC 57.363 43.478 6.65 0.00 44.19 2.50
263 267 5.061684 TGACGATGTTTTCAGCATAACTACG 59.938 40.000 0.00 0.00 35.78 3.51
305 309 8.437742 GTTTTGGACTCTAATTTGCATGATTTG 58.562 33.333 0.00 0.00 0.00 2.32
336 340 5.252547 AGCCACTTTTCCAAACAATTTTGT 58.747 33.333 0.00 0.00 44.72 2.83
355 359 4.202182 GGTGATACGTCCTAAATGTAGCCA 60.202 45.833 0.00 0.00 35.34 4.75
358 362 3.979495 GCGGTGATACGTCCTAAATGTAG 59.021 47.826 0.00 0.00 32.91 2.74
362 366 1.677576 TCGCGGTGATACGTCCTAAAT 59.322 47.619 6.13 0.00 35.98 1.40
388 395 7.081349 CGGCAGTAATGAAAATACTTTGTTGA 58.919 34.615 0.00 0.00 31.33 3.18
409 416 0.679640 CTAAAGGGTGATTGCCGGCA 60.680 55.000 29.03 29.03 0.00 5.69
410 417 1.384222 CCTAAAGGGTGATTGCCGGC 61.384 60.000 22.73 22.73 0.00 6.13
435 442 0.944386 GTTTTCTCTGAACTGGCGCA 59.056 50.000 10.83 0.00 0.00 6.09
441 448 5.586643 GGAAGTTGTCAGTTTTCTCTGAACT 59.413 40.000 0.00 0.00 44.48 3.01
464 471 0.033796 ACTGGATGGGCTGATGTTGG 60.034 55.000 0.00 0.00 0.00 3.77
475 482 1.487976 AGCCTACACATGACTGGATGG 59.512 52.381 0.00 0.00 0.00 3.51
488 495 3.070159 GTGAAGCTATGATCCAGCCTACA 59.930 47.826 11.67 7.77 39.99 2.74
489 496 3.070159 TGTGAAGCTATGATCCAGCCTAC 59.930 47.826 11.67 9.37 39.99 3.18
511 518 3.737559 TGGGGCTTGATGTTTATCTGT 57.262 42.857 0.00 0.00 34.31 3.41
516 523 2.228545 TGCATGGGGCTTGATGTTTA 57.771 45.000 0.00 0.00 45.15 2.01
587 594 0.254178 CTCCTAGTGCTTGCACCCAT 59.746 55.000 20.39 6.66 0.00 4.00
601 608 0.253327 TCTCTGCTGCGAGTCTCCTA 59.747 55.000 16.79 0.05 32.83 2.94
702 710 2.670592 GTTTAGCCGGCCCGTTGT 60.671 61.111 26.15 5.68 0.00 3.32
704 712 2.248086 CTAGGTTTAGCCGGCCCGTT 62.248 60.000 26.15 7.06 43.70 4.44
705 713 2.684655 TAGGTTTAGCCGGCCCGT 60.685 61.111 26.15 7.52 43.70 5.28
744 753 2.464016 GCAAAGCGTTTTTCTTCTCGTG 59.536 45.455 0.00 0.00 0.00 4.35
783 792 4.846779 AAAATGTACACATCAAAGCGGT 57.153 36.364 0.00 0.00 35.10 5.68
1042 1358 3.356639 GAGCCTGATGCCGTCGTGA 62.357 63.158 0.00 0.00 42.71 4.35
1043 1359 2.887568 GAGCCTGATGCCGTCGTG 60.888 66.667 0.00 0.00 42.71 4.35
1044 1360 4.148825 GGAGCCTGATGCCGTCGT 62.149 66.667 0.00 0.00 42.71 4.34
1254 1571 0.616395 TAGGGCTTGACATCGTGGGA 60.616 55.000 0.00 0.00 0.00 4.37
1337 1654 2.735237 GGGCGAAGGATACCGGAG 59.265 66.667 9.46 0.00 37.17 4.63
1564 2164 7.539366 GTCATTCAATCGTATAAGCCTAGAGAC 59.461 40.741 0.00 0.00 0.00 3.36
1978 2580 4.399303 ACGGCAAGCTAGAGCATTTAAATT 59.601 37.500 4.01 0.00 45.16 1.82
1990 2592 3.877508 AGCCTAATTAAACGGCAAGCTAG 59.122 43.478 14.66 0.00 46.14 3.42
2062 2664 3.785887 AGGAAATCATGGTACCTTAGCCA 59.214 43.478 14.36 0.00 39.33 4.75
2271 2873 1.955080 GCTAGCCTTACCTCTTAGCGA 59.045 52.381 2.29 0.00 0.00 4.93
2485 3087 4.171005 CAAACAAACATCTATGCTGCCAG 58.829 43.478 0.00 0.00 0.00 4.85
2546 3148 4.496341 GGAAAACATGGACGCATCATAGTG 60.496 45.833 0.00 0.00 0.00 2.74
2604 3206 0.031994 ATTGTTGCTGGCCGTTGAAC 59.968 50.000 0.00 0.00 0.00 3.18
2810 3412 5.064707 AGTCGACATTGCCATGTTAATACAC 59.935 40.000 19.50 0.00 44.22 2.90
2811 3413 5.182487 AGTCGACATTGCCATGTTAATACA 58.818 37.500 19.50 0.00 44.22 2.29
2812 3414 5.734855 AGTCGACATTGCCATGTTAATAC 57.265 39.130 19.50 2.15 44.22 1.89
2813 3415 5.645929 ACAAGTCGACATTGCCATGTTAATA 59.354 36.000 19.50 0.00 44.22 0.98
2814 3416 4.458989 ACAAGTCGACATTGCCATGTTAAT 59.541 37.500 19.50 0.00 44.22 1.40
2889 3491 8.700051 TCTGAAGATGGGAAAACATTTAAACAA 58.300 29.630 0.00 0.00 0.00 2.83
3039 3641 0.810648 TTGCCCATCAACGCTCAATC 59.189 50.000 0.00 0.00 0.00 2.67
3047 3649 1.270550 CACCAGTTCTTGCCCATCAAC 59.729 52.381 0.00 0.00 0.00 3.18
3097 3699 2.817258 TCAAATCCACCGATTCCACAAC 59.183 45.455 0.00 0.00 37.76 3.32
3288 3908 9.731001 CCTATTATTAGGTTATATCCAGGTCCT 57.269 37.037 2.69 0.00 40.28 3.85
3557 4999 7.148623 GGAAAGTATTATTCTAATCCTTCGGCG 60.149 40.741 0.00 0.00 0.00 6.46
3598 5040 6.645884 AATCCCTAATACCCTAACACAACA 57.354 37.500 0.00 0.00 0.00 3.33
3800 6342 2.307980 AGGTTAGGGTAGGTGCTTTTCC 59.692 50.000 0.00 0.00 0.00 3.13
3806 6348 3.244805 ACAAGAAAGGTTAGGGTAGGTGC 60.245 47.826 0.00 0.00 0.00 5.01
3847 6389 5.830457 TGAACAATGGTACCACTTGAATTCA 59.170 36.000 28.70 25.16 0.00 2.57
3848 6390 6.016276 ACTGAACAATGGTACCACTTGAATTC 60.016 38.462 28.70 23.79 0.00 2.17
3849 6391 5.833131 ACTGAACAATGGTACCACTTGAATT 59.167 36.000 28.70 19.44 0.00 2.17
3850 6392 5.385198 ACTGAACAATGGTACCACTTGAAT 58.615 37.500 28.70 20.98 0.00 2.57
3851 6393 4.787551 ACTGAACAATGGTACCACTTGAA 58.212 39.130 28.70 18.34 0.00 2.69
3852 6394 4.141597 TGACTGAACAATGGTACCACTTGA 60.142 41.667 28.70 13.08 0.00 3.02
3853 6395 4.133820 TGACTGAACAATGGTACCACTTG 58.866 43.478 19.09 22.39 0.00 3.16
3854 6396 4.431416 TGACTGAACAATGGTACCACTT 57.569 40.909 19.09 8.93 0.00 3.16
3855 6397 4.640771 ATGACTGAACAATGGTACCACT 57.359 40.909 19.09 2.12 0.00 4.00
3856 6398 4.759693 TCAATGACTGAACAATGGTACCAC 59.240 41.667 19.09 4.41 0.00 4.16
3857 6399 4.979335 TCAATGACTGAACAATGGTACCA 58.021 39.130 18.99 18.99 0.00 3.25
3858 6400 5.957842 TTCAATGACTGAACAATGGTACC 57.042 39.130 4.43 4.43 39.20 3.34
3859 6401 9.722056 GATAATTCAATGACTGAACAATGGTAC 57.278 33.333 0.00 0.00 46.80 3.34
3860 6402 9.685276 AGATAATTCAATGACTGAACAATGGTA 57.315 29.630 0.00 0.00 46.80 3.25
3861 6403 8.464404 CAGATAATTCAATGACTGAACAATGGT 58.536 33.333 0.00 0.00 46.80 3.55
3862 6404 8.464404 ACAGATAATTCAATGACTGAACAATGG 58.536 33.333 5.05 0.00 46.80 3.16
3863 6405 9.850628 AACAGATAATTCAATGACTGAACAATG 57.149 29.630 5.05 0.00 46.80 2.82
3866 6408 9.725019 AGTAACAGATAATTCAATGACTGAACA 57.275 29.630 5.05 0.00 46.80 3.18
3867 6409 9.979270 CAGTAACAGATAATTCAATGACTGAAC 57.021 33.333 5.05 3.54 46.80 3.18
3869 6411 9.154847 CACAGTAACAGATAATTCAATGACTGA 57.845 33.333 5.05 0.00 35.63 3.41
3870 6412 8.939929 ACACAGTAACAGATAATTCAATGACTG 58.060 33.333 0.00 0.00 37.26 3.51
3871 6413 8.939929 CACACAGTAACAGATAATTCAATGACT 58.060 33.333 0.00 0.00 0.00 3.41
3872 6414 7.693951 GCACACAGTAACAGATAATTCAATGAC 59.306 37.037 0.00 0.00 0.00 3.06
3873 6415 7.390162 TGCACACAGTAACAGATAATTCAATGA 59.610 33.333 0.00 0.00 0.00 2.57
3874 6416 7.529158 TGCACACAGTAACAGATAATTCAATG 58.471 34.615 0.00 0.00 0.00 2.82
3875 6417 7.686438 TGCACACAGTAACAGATAATTCAAT 57.314 32.000 0.00 0.00 0.00 2.57
3876 6418 7.686438 ATGCACACAGTAACAGATAATTCAA 57.314 32.000 0.00 0.00 0.00 2.69
3950 6492 1.218875 TTGAACACGGCACTAGCACG 61.219 55.000 0.00 0.00 44.61 5.34
4027 6570 6.815142 ACTAAATCATGCAGGATTTTCAAAGC 59.185 34.615 35.67 0.00 43.13 3.51
4048 6591 6.823689 GCCTCCTTGAAATGTGATTAGACTAA 59.176 38.462 0.00 0.00 0.00 2.24
4886 7433 4.774726 TCCACTTCTCTATGCTTGAGTTCT 59.225 41.667 0.00 0.00 33.59 3.01
4979 7526 1.203013 TCCTTCTCACGGTCCTTCTCA 60.203 52.381 0.00 0.00 0.00 3.27
5078 7625 1.071605 CAAGTGCGTTACTGCTCCTC 58.928 55.000 0.00 0.00 40.26 3.71
5268 7815 1.372087 GGTGCATCTGCTTCCTTCCG 61.372 60.000 3.53 0.00 42.66 4.30
5881 8428 6.349300 TGTTCTCTAACTTGGGCTTATCATC 58.651 40.000 0.00 0.00 36.51 2.92
6135 8682 8.107095 ACATACCTAAACTGCTTCCATAAAGAA 58.893 33.333 0.00 0.00 37.12 2.52
6136 8683 7.630082 ACATACCTAAACTGCTTCCATAAAGA 58.370 34.615 0.00 0.00 37.12 2.52
6137 8684 7.865706 ACATACCTAAACTGCTTCCATAAAG 57.134 36.000 0.00 0.00 38.08 1.85
6165 8712 5.346551 GCGTTTTTCTTTTTGTAACCACTGT 59.653 36.000 0.00 0.00 0.00 3.55
6529 9076 4.722526 TTCCTCCTCACCAAGAAATTCA 57.277 40.909 0.00 0.00 0.00 2.57
6628 9175 0.721718 CAGCCTCGACGTCCAAAATC 59.278 55.000 10.58 0.00 0.00 2.17
6832 9379 4.806247 GGAACCAGTAATTCGATCTCACTG 59.194 45.833 9.00 9.00 37.06 3.66
6957 9504 5.770162 ACCTGTTGGAACTTGGAAAAGATAG 59.230 40.000 8.44 0.00 37.04 2.08
6961 9508 3.699038 TCACCTGTTGGAACTTGGAAAAG 59.301 43.478 8.44 0.00 37.04 2.27
6962 9509 3.702792 TCACCTGTTGGAACTTGGAAAA 58.297 40.909 8.44 0.00 37.04 2.29
7073 9620 4.567159 ACACTCTCAAAGTCTCGTGAAAAC 59.433 41.667 0.00 0.00 35.45 2.43
7080 9627 4.861210 ACAAGTACACTCTCAAAGTCTCG 58.139 43.478 0.00 0.00 35.45 4.04
7091 9638 9.615295 TTTTGTTGAAGTAAAACAAGTACACTC 57.385 29.630 0.00 0.00 45.47 3.51
7208 9756 3.980646 TTGCAAACGCACAGAAGTTAT 57.019 38.095 0.00 0.00 39.71 1.89
7217 9765 5.390613 AGAATACTACAATTGCAAACGCAC 58.609 37.500 1.71 0.00 39.71 5.34
7305 9896 5.867716 GCGGAGAAGTTAGATTTCTTACACA 59.132 40.000 0.21 0.00 35.14 3.72
7326 9917 0.171007 CAATTGCAACCACTAGGCGG 59.829 55.000 0.00 0.00 39.06 6.13
7328 9919 3.081804 ACTACAATTGCAACCACTAGGC 58.918 45.455 0.00 0.00 39.06 3.93
7336 9927 5.001232 TCACCCTAGAACTACAATTGCAAC 58.999 41.667 0.00 0.00 0.00 4.17
7416 10014 2.854805 GCAAACACAAGGCGAAGAAGTC 60.855 50.000 0.00 0.00 0.00 3.01
7533 10133 7.395489 AGTCCAAACAAGAGCATATGATTCTTT 59.605 33.333 16.04 8.57 0.00 2.52
7534 10134 6.888632 AGTCCAAACAAGAGCATATGATTCTT 59.111 34.615 6.97 11.44 0.00 2.52
7535 10135 6.421485 AGTCCAAACAAGAGCATATGATTCT 58.579 36.000 6.97 5.64 0.00 2.40
7536 10136 6.690194 AGTCCAAACAAGAGCATATGATTC 57.310 37.500 6.97 3.21 0.00 2.52
7542 10142 8.691797 AGTTTTTAAAGTCCAAACAAGAGCATA 58.308 29.630 3.31 0.00 33.58 3.14
7563 10163 7.015195 AGGCCACAAATAATACTGTCAAGTTTT 59.985 33.333 5.01 0.00 37.88 2.43
7574 10174 9.869757 ACAAATTCTTTAGGCCACAAATAATAC 57.130 29.630 5.01 0.00 0.00 1.89
7637 10238 5.637006 TGTGTACAGTTCAGTTTTGCTTT 57.363 34.783 0.00 0.00 0.00 3.51
7666 10267 7.661027 GGAAAAATCTCAATGAATTCAACCCAA 59.339 33.333 13.09 0.00 0.00 4.12
7791 10392 7.501559 ACATATTGATCTTTGATGGTCTCCAAG 59.498 37.037 0.00 0.00 36.95 3.61
7843 10444 8.587608 TGTTCTTCCATCTTTAAAATTCTGCAT 58.412 29.630 0.00 0.00 0.00 3.96
7896 10497 3.243267 GGTTGTTAGCACGGAACACAAAT 60.243 43.478 0.00 0.00 36.55 2.32
7917 10518 2.706339 AGCTAACTGGAATGCAGAGG 57.294 50.000 9.20 0.00 0.00 3.69
7918 10519 3.755378 ACAAAGCTAACTGGAATGCAGAG 59.245 43.478 9.20 0.00 0.00 3.35
7919 10520 3.754965 ACAAAGCTAACTGGAATGCAGA 58.245 40.909 9.20 0.00 0.00 4.26
7931 10532 7.166804 GCAACAATAAAAGACGAACAAAGCTAA 59.833 33.333 0.00 0.00 0.00 3.09


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

AutoCloner maintained by Alex Coulton.