Multiple sequence alignment - TraesCS3D01G362000

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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 TraesCS3D01G362000 chr3D 100.000 5801 0 0 1 5801 476194692 476200492 0.000000e+00 10713
1 TraesCS3D01G362000 chr3D 88.269 520 54 5 1976 2493 445757418 445756904 2.970000e-172 616
2 TraesCS3D01G362000 chr3D 86.911 191 14 1 2805 2995 445756058 445755879 2.740000e-48 204
3 TraesCS3D01G362000 chr3A 93.632 3329 136 21 556 3876 619645998 619649258 0.000000e+00 4903
4 TraesCS3D01G362000 chr3A 94.284 1557 52 17 3929 5459 619649257 619650802 0.000000e+00 2348
5 TraesCS3D01G362000 chr3A 84.282 439 62 5 1 433 619644754 619645191 6.950000e-114 422
6 TraesCS3D01G362000 chr3A 94.355 124 7 0 426 549 619645739 619645862 2.130000e-44 191
7 TraesCS3D01G362000 chr3A 90.909 88 7 1 5543 5630 507291575 507291489 3.670000e-22 117
8 TraesCS3D01G362000 chr3B 94.932 1835 73 11 3982 5801 634235024 634233195 0.000000e+00 2856
9 TraesCS3D01G362000 chr3B 94.858 1731 74 10 1229 2952 634237747 634236025 0.000000e+00 2689
10 TraesCS3D01G362000 chr3B 92.811 932 51 7 3056 3977 634236034 634235109 0.000000e+00 1336
11 TraesCS3D01G362000 chr3B 91.024 791 48 6 370 1141 634238948 634238162 0.000000e+00 1046
12 TraesCS3D01G362000 chr3B 85.401 274 33 6 1 270 634239232 634238962 1.590000e-70 278
13 TraesCS3D01G362000 chr5B 88.484 521 54 4 1975 2493 599604478 599603962 4.940000e-175 625
14 TraesCS3D01G362000 chr5B 87.037 216 14 3 2805 3019 599603120 599602918 1.260000e-56 231
15 TraesCS3D01G362000 chr5B 86.170 94 11 2 5543 5636 217907682 217907773 3.700000e-17 100
16 TraesCS3D01G362000 chr1D 88.292 521 54 5 1975 2493 475274688 475274173 8.260000e-173 617
17 TraesCS3D01G362000 chr5A 86.948 521 62 4 1975 2493 55378564 55378048 1.080000e-161 580
18 TraesCS3D01G362000 chr5A 86.099 223 14 5 2832 3050 55377176 55376967 2.100000e-54 224
19 TraesCS3D01G362000 chrUn 86.513 519 65 4 1975 2493 36554262 36554775 3.030000e-157 566
20 TraesCS3D01G362000 chrUn 85.714 280 31 6 2799 3077 36555629 36555900 2.650000e-73 287
21 TraesCS3D01G362000 chr6D 84.848 198 13 4 2805 3001 810460 810279 3.570000e-42 183
22 TraesCS3D01G362000 chr6D 87.912 91 9 2 5544 5634 142148799 142148711 7.950000e-19 106
23 TraesCS3D01G362000 chr6D 85.859 99 11 3 5544 5641 142148715 142148811 1.030000e-17 102
24 TraesCS3D01G362000 chr1A 90.110 91 8 1 5542 5632 474384834 474384745 3.670000e-22 117
25 TraesCS3D01G362000 chr1A 90.476 84 8 0 5542 5625 583304729 583304646 1.710000e-20 111
26 TraesCS3D01G362000 chr5D 87.234 94 10 2 5543 5636 188826534 188826625 7.950000e-19 106
27 TraesCS3D01G362000 chr2D 88.636 88 9 1 5543 5630 512165839 512165925 7.950000e-19 106


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 TraesCS3D01G362000 chr3D 476194692 476200492 5800 False 10713.0 10713 100.00000 1 5801 1 chr3D.!!$F1 5800
1 TraesCS3D01G362000 chr3D 445755879 445757418 1539 True 410.0 616 87.59000 1976 2995 2 chr3D.!!$R1 1019
2 TraesCS3D01G362000 chr3A 619644754 619650802 6048 False 1966.0 4903 91.63825 1 5459 4 chr3A.!!$F1 5458
3 TraesCS3D01G362000 chr3B 634233195 634239232 6037 True 1641.0 2856 91.80520 1 5801 5 chr3B.!!$R1 5800
4 TraesCS3D01G362000 chr5B 599602918 599604478 1560 True 428.0 625 87.76050 1975 3019 2 chr5B.!!$R1 1044
5 TraesCS3D01G362000 chr1D 475274173 475274688 515 True 617.0 617 88.29200 1975 2493 1 chr1D.!!$R1 518
6 TraesCS3D01G362000 chr5A 55376967 55378564 1597 True 402.0 580 86.52350 1975 3050 2 chr5A.!!$R1 1075
7 TraesCS3D01G362000 chrUn 36554262 36555900 1638 False 426.5 566 86.11350 1975 3077 2 chrUn.!!$F1 1102

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
920 1620 0.043334 CTCCTCCCTCCCCTCTCAAA 59.957 60.000 0.00 0.0 0.00 2.69 F
943 1643 1.003233 CGCTTAGTTCCTCCCCAACTT 59.997 52.381 0.00 0.0 35.63 2.66 F
1890 2922 1.368641 CAAGGTACGCATTGCTGCTA 58.631 50.000 7.12 0.0 46.65 3.49 F
2167 3200 0.813184 CATCGCTTGCCAGATTGGTT 59.187 50.000 0.00 0.0 40.46 3.67 F
3013 4739 0.037590 TTGGCACCCAATCGTAAGCT 59.962 50.000 0.00 0.0 38.75 3.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1918 2950 0.465705 TGATCGATCAGCTTGGGGAC 59.534 55.000 23.99 0.00 32.11 4.46 R
2150 3183 0.537143 ACAACCAATCTGGCAAGCGA 60.537 50.000 0.00 0.00 42.67 4.93 R
2995 4721 0.906066 TAGCTTACGATTGGGTGCCA 59.094 50.000 0.00 0.00 0.00 4.92 R
3175 4913 1.597302 CGGAGCATCAGCATCCCTG 60.597 63.158 0.00 0.00 45.49 4.45 R
5007 6840 0.240145 TAACCAGCAGACGACTGACG 59.760 55.000 19.07 7.91 46.03 4.35 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
37 38 2.161030 GTGTGTCGGAGAGTAGGAAGT 58.839 52.381 0.00 0.00 36.95 3.01
71 72 4.917906 AAGTAGCAAAAGGGAGTCTGAT 57.082 40.909 0.00 0.00 0.00 2.90
106 107 1.227380 AGAGCTAAAGATGCGGCGG 60.227 57.895 9.78 0.00 35.28 6.13
107 108 1.521681 GAGCTAAAGATGCGGCGGT 60.522 57.895 9.78 0.00 35.28 5.68
123 124 3.005539 GTGCAGGAGAGGGGAGCA 61.006 66.667 0.00 0.00 0.00 4.26
145 146 0.598065 CGGGTTCTGGAAGGCAAAAG 59.402 55.000 0.00 0.00 0.00 2.27
149 150 3.222603 GGTTCTGGAAGGCAAAAGAGAA 58.777 45.455 0.00 0.00 0.00 2.87
151 152 4.261783 GGTTCTGGAAGGCAAAAGAGAAAG 60.262 45.833 0.00 0.00 0.00 2.62
152 153 3.490348 TCTGGAAGGCAAAAGAGAAAGG 58.510 45.455 0.00 0.00 0.00 3.11
153 154 2.560105 CTGGAAGGCAAAAGAGAAAGGG 59.440 50.000 0.00 0.00 0.00 3.95
196 199 0.625849 GATGGGGATTGTGTGGGAGT 59.374 55.000 0.00 0.00 0.00 3.85
221 225 2.444256 GCGGCCCCAGATAAGGACT 61.444 63.158 0.00 0.00 0.00 3.85
229 233 1.278985 CCAGATAAGGACTGGTGCACA 59.721 52.381 20.43 3.92 46.71 4.57
256 261 2.742372 GAATGCGTGGGTGAGCGT 60.742 61.111 0.00 0.00 35.87 5.07
261 266 2.738521 CGTGGGTGAGCGTGAAGG 60.739 66.667 0.00 0.00 0.00 3.46
268 273 1.540363 GGTGAGCGTGAAGGAAAGTGA 60.540 52.381 0.00 0.00 0.00 3.41
269 274 1.527311 GTGAGCGTGAAGGAAAGTGAC 59.473 52.381 0.00 0.00 0.00 3.67
272 277 2.600388 CGTGAAGGAAAGTGACGCA 58.400 52.632 0.00 0.00 0.00 5.24
299 304 2.202676 GAGAGCAAGCTCGGACCG 60.203 66.667 15.67 7.84 46.90 4.79
300 305 2.992114 AGAGCAAGCTCGGACCGT 60.992 61.111 14.79 0.00 46.90 4.83
301 306 2.048127 GAGCAAGCTCGGACCGTT 60.048 61.111 14.79 0.00 33.06 4.44
303 308 3.479269 GCAAGCTCGGACCGTTCG 61.479 66.667 14.79 5.05 0.00 3.95
304 309 2.257371 CAAGCTCGGACCGTTCGA 59.743 61.111 14.79 1.08 35.24 3.71
308 313 1.372623 GCTCGGACCGTTCGAAAGT 60.373 57.895 14.79 6.08 36.15 2.66
321 326 1.217882 CGAAAGTTCGGTCAGCTGTT 58.782 50.000 14.67 0.00 46.30 3.16
348 353 8.805688 CGATTTTAAACGTTTCCCAAAAACTTA 58.194 29.630 18.42 0.00 0.00 2.24
352 357 8.999220 TTAAACGTTTCCCAAAAACTTAACAT 57.001 26.923 18.42 0.00 0.00 2.71
374 379 9.662947 AACATACCTAAAAATACGAGTTAGCTT 57.337 29.630 0.00 0.00 0.00 3.74
384 389 0.909623 GAGTTAGCTTACTGCCCCCA 59.090 55.000 10.67 0.00 44.23 4.96
392 397 3.011257 AGCTTACTGCCCCCATTTTCTTA 59.989 43.478 0.00 0.00 44.23 2.10
441 1003 6.587608 CGCTCATAGGCAAAGAAGAAAAATTT 59.412 34.615 0.00 0.00 0.00 1.82
442 1004 7.411157 CGCTCATAGGCAAAGAAGAAAAATTTG 60.411 37.037 0.00 0.00 37.07 2.32
451 1013 9.636965 GCAAAGAAGAAAAATTTGAATACACAC 57.363 29.630 0.00 0.00 36.28 3.82
538 1100 2.639286 CAGGTTTGTGTCGCCAGC 59.361 61.111 0.00 0.00 0.00 4.85
549 1111 1.957186 TCGCCAGCACGTTGTTACC 60.957 57.895 0.00 0.00 0.00 2.85
550 1112 2.248135 CGCCAGCACGTTGTTACCA 61.248 57.895 0.00 0.00 0.00 3.25
551 1113 1.281656 GCCAGCACGTTGTTACCAC 59.718 57.895 0.00 0.00 0.00 4.16
552 1114 1.440938 GCCAGCACGTTGTTACCACA 61.441 55.000 0.00 0.00 0.00 4.17
554 1116 1.606668 CCAGCACGTTGTTACCACATT 59.393 47.619 0.00 0.00 31.06 2.71
558 1250 2.136728 CACGTTGTTACCACATTCGGA 58.863 47.619 0.00 0.00 35.95 4.55
575 1267 0.953960 GGAAGGCGTCGGTGTGAAAT 60.954 55.000 0.00 0.00 0.00 2.17
625 1317 4.449068 TCAGATCGAAGCTGTTTCTCAAAC 59.551 41.667 15.55 0.00 41.73 2.93
746 1445 7.430502 GCATATTTTTCCATTTCTGAAGAGTCG 59.569 37.037 0.00 0.00 0.00 4.18
752 1451 3.933332 CCATTTCTGAAGAGTCGTTACCC 59.067 47.826 0.00 0.00 0.00 3.69
808 1508 2.621000 CAGCGCGCGTTCTAATCC 59.379 61.111 32.35 11.90 0.00 3.01
809 1509 2.585247 AGCGCGCGTTCTAATCCC 60.585 61.111 32.35 11.09 0.00 3.85
810 1510 2.888534 GCGCGCGTTCTAATCCCA 60.889 61.111 32.35 0.00 0.00 4.37
844 1544 2.604174 CCGCGCGAAGTCCAAAACT 61.604 57.895 34.63 0.00 41.10 2.66
920 1620 0.043334 CTCCTCCCTCCCCTCTCAAA 59.957 60.000 0.00 0.00 0.00 2.69
926 1626 2.203938 TCCCCTCTCAAACCCGCT 60.204 61.111 0.00 0.00 0.00 5.52
927 1627 1.842381 CTCCCCTCTCAAACCCGCTT 61.842 60.000 0.00 0.00 0.00 4.68
943 1643 1.003233 CGCTTAGTTCCTCCCCAACTT 59.997 52.381 0.00 0.00 35.63 2.66
1165 1865 2.890474 CCGATTCGCCCCAGTTCG 60.890 66.667 0.00 0.00 0.00 3.95
1258 2290 5.863397 TCCGCTTCATTTCATTTCATTTCAC 59.137 36.000 0.00 0.00 0.00 3.18
1262 2294 7.115236 CGCTTCATTTCATTTCATTTCACTTCA 59.885 33.333 0.00 0.00 0.00 3.02
1281 2313 1.395954 CACATCTCCTGACAATGTGCG 59.604 52.381 5.31 0.00 42.51 5.34
1567 2599 1.966451 CCTGGTTTGCAGGGACGAC 60.966 63.158 0.00 0.00 36.22 4.34
1722 2754 3.521531 TGGGCTGATGAGGTACATTACAA 59.478 43.478 0.00 0.00 39.56 2.41
1724 2756 4.384208 GGGCTGATGAGGTACATTACAAGT 60.384 45.833 0.00 0.00 39.56 3.16
1742 2774 6.639632 ACAAGTTTTCAGTATGTGAGCAAT 57.360 33.333 0.00 0.00 36.21 3.56
1761 2793 6.051074 AGCAATTTTCTCTGTTTCAAAAGGG 58.949 36.000 0.00 0.00 0.00 3.95
1791 2823 5.065859 TGTCAAATCGTGTGTCATTTGTCTT 59.934 36.000 5.29 0.00 39.84 3.01
1890 2922 1.368641 CAAGGTACGCATTGCTGCTA 58.631 50.000 7.12 0.00 46.65 3.49
1918 2950 7.587037 TTATGGGCTCAAATCTTCTTATTGG 57.413 36.000 0.00 0.00 0.00 3.16
1919 2951 4.934356 TGGGCTCAAATCTTCTTATTGGT 58.066 39.130 0.00 0.00 0.00 3.67
1952 2984 7.454260 TGATCGATCATGCAGTACTAATAGT 57.546 36.000 23.99 0.00 0.00 2.12
2129 3162 5.273523 GCTTTTCTTGCCATTTTGATCAC 57.726 39.130 0.00 0.00 0.00 3.06
2130 3163 4.751098 GCTTTTCTTGCCATTTTGATCACA 59.249 37.500 0.00 0.00 0.00 3.58
2150 3183 7.410120 TCACACTATCTGAACTGTATGTCAT 57.590 36.000 0.00 0.00 0.00 3.06
2167 3200 0.813184 CATCGCTTGCCAGATTGGTT 59.187 50.000 0.00 0.00 40.46 3.67
2282 3315 7.549488 GCATACTGATAGGTTAGTTTTCTGTGT 59.451 37.037 0.00 0.00 0.00 3.72
2375 3410 4.377021 ACTGTTTTGCTAACTGATCGTCA 58.623 39.130 13.23 0.00 0.00 4.35
2436 3471 3.126000 CAGATCGGTTTCTTCCAAAGCTC 59.874 47.826 0.00 0.00 0.00 4.09
2476 3511 9.482627 GTAAGCATTCTTACTATATCTGCTGTT 57.517 33.333 7.88 0.00 46.93 3.16
2779 4505 6.402222 ACAGGTTCTTGAGTATGATGTCTTC 58.598 40.000 0.00 0.00 0.00 2.87
2821 4547 2.176889 TGTGCTAGGGTAAGTCCAGTC 58.823 52.381 0.00 0.00 38.11 3.51
2937 4663 1.493022 ACCAAACACTGAAGGTAGGCA 59.507 47.619 0.00 0.00 31.32 4.75
2971 4697 4.611310 CACCAATGCTAAGTGATGTGAG 57.389 45.455 0.00 0.00 33.21 3.51
2978 4704 2.483889 GCTAAGTGATGTGAGGGTAGGC 60.484 54.545 0.00 0.00 0.00 3.93
3007 4733 2.524569 AAAAACTTGGCACCCAATCG 57.475 45.000 0.00 0.00 43.07 3.34
3008 4734 1.408969 AAAACTTGGCACCCAATCGT 58.591 45.000 0.00 0.00 43.07 3.73
3009 4735 2.279935 AAACTTGGCACCCAATCGTA 57.720 45.000 0.00 0.00 43.07 3.43
3010 4736 2.279935 AACTTGGCACCCAATCGTAA 57.720 45.000 0.00 0.00 43.07 3.18
3011 4737 1.821216 ACTTGGCACCCAATCGTAAG 58.179 50.000 0.00 0.00 43.07 2.34
3012 4738 0.451783 CTTGGCACCCAATCGTAAGC 59.548 55.000 0.00 0.00 43.07 3.09
3013 4739 0.037590 TTGGCACCCAATCGTAAGCT 59.962 50.000 0.00 0.00 38.75 3.74
3086 4812 5.346822 GCAAAATCAGAAGTATTTGTGCCTG 59.653 40.000 0.00 0.00 35.68 4.85
3134 4864 9.457436 GTAAACTGATCTTAAATGGGGTTTAGA 57.543 33.333 0.00 0.00 33.99 2.10
3312 5050 8.200792 TGTTTGCAGGTAATTTATTTCTTGTGT 58.799 29.630 0.00 0.00 0.00 3.72
3357 5095 7.838079 TGCAATCTGCCACCTTTATTATTAT 57.162 32.000 0.00 0.00 44.23 1.28
3409 5147 4.943705 TGTTGAAAGAGTTCTGGATATGGC 59.056 41.667 0.00 0.00 34.60 4.40
3514 5252 7.713073 GGACTACAAGATTCTTCTGATAAAGGG 59.287 40.741 0.00 0.00 30.72 3.95
3565 5303 5.824624 TCATGTTTATTTTTGCTTTGGCCAA 59.175 32.000 16.05 16.05 37.74 4.52
3581 5319 7.468494 GCTTTGGCCAAGAATGTTTAAATTTGT 60.468 33.333 19.48 0.00 33.80 2.83
3635 5373 6.996509 TCTGTAGCTCATATGCACAATGATA 58.003 36.000 12.62 3.07 33.08 2.15
3636 5374 6.870439 TCTGTAGCTCATATGCACAATGATAC 59.130 38.462 12.62 12.91 33.08 2.24
3759 5497 4.005650 TGAATCTTGACTGGTGCTTCATC 58.994 43.478 0.00 0.00 0.00 2.92
3799 5537 7.738437 ATTCCCAAATGACCAACTGATATTT 57.262 32.000 0.00 0.00 0.00 1.40
3812 5550 7.178983 ACCAACTGATATTTGAACAACATCCAT 59.821 33.333 0.00 0.00 0.00 3.41
3867 5605 4.202357 TGCTGTGTTCTAAATCCTCAGTGT 60.202 41.667 0.00 0.00 0.00 3.55
3870 5608 6.413783 TGTGTTCTAAATCCTCAGTGTACA 57.586 37.500 0.00 0.00 0.00 2.90
3888 5627 8.076178 CAGTGTACAAATTACCTTTTTGAGAGG 58.924 37.037 0.00 0.00 37.48 3.69
3891 5630 9.362151 TGTACAAATTACCTTTTTGAGAGGATT 57.638 29.630 0.00 0.00 37.48 3.01
3904 5643 7.487822 TTTGAGAGGATTCTACAGAACAGAT 57.512 36.000 0.00 0.00 36.80 2.90
3913 5652 7.497249 GGATTCTACAGAACAGATAACATGCTT 59.503 37.037 0.00 0.00 36.80 3.91
3915 5654 8.621532 TTCTACAGAACAGATAACATGCTTTT 57.378 30.769 0.00 0.00 0.00 2.27
3936 5675 5.675684 TTGCTGTGTTCCTGTATCTGATA 57.324 39.130 0.00 0.00 0.00 2.15
4004 5825 4.081862 TGTTATCTCTTCTTACACCCCACG 60.082 45.833 0.00 0.00 0.00 4.94
4054 5875 8.906867 CATAAATTCTACCAGGTGACATTTGAT 58.093 33.333 0.76 0.00 0.00 2.57
4330 6151 3.671928 GCATTCTGAATGAACACACTTGC 59.328 43.478 29.34 11.25 41.46 4.01
4335 6156 4.883585 TCTGAATGAACACACTTGCTCTTT 59.116 37.500 0.00 0.00 0.00 2.52
4498 6319 1.670811 GATCAGGTATGCAAACACCCG 59.329 52.381 10.88 2.87 35.25 5.28
4679 6504 2.227865 TGCATTTAAGGTGCGGAAAGAC 59.772 45.455 9.47 0.00 45.37 3.01
4687 6512 1.066136 GTGCGGAAAGACGGTCTTAC 58.934 55.000 22.67 17.02 35.27 2.34
4689 6514 1.068055 TGCGGAAAGACGGTCTTACTC 60.068 52.381 22.67 16.86 35.27 2.59
4935 6763 1.523938 GTATGCTGCTCCCCGTTCC 60.524 63.158 0.00 0.00 0.00 3.62
4949 6777 3.244457 CCCCGTTCCATAGATTCCTTACC 60.244 52.174 0.00 0.00 0.00 2.85
4982 6810 7.653311 GTCTTTATTTTGTTGAATCAGGTGCTT 59.347 33.333 0.00 0.00 0.00 3.91
4983 6811 7.652909 TCTTTATTTTGTTGAATCAGGTGCTTG 59.347 33.333 0.00 0.00 0.00 4.01
5007 6840 6.591062 TGCATTCATTGTATCAAGCTTTTTCC 59.409 34.615 0.00 0.00 0.00 3.13
5122 6955 5.316987 ACAGTTCCTCCAAAAGATAGTTGG 58.683 41.667 0.00 0.00 45.89 3.77
5315 7153 8.519799 TCCCCTGTGAGATAAACATAATTTTC 57.480 34.615 0.00 0.00 0.00 2.29
5326 7164 9.971922 GATAAACATAATTTTCCTGAGGAATGG 57.028 33.333 15.75 4.06 41.71 3.16
5328 7166 4.651045 ACATAATTTTCCTGAGGAATGGCC 59.349 41.667 15.75 0.00 41.71 5.36
5378 7225 3.063510 TCAGCTTGACTCCAAATCCAG 57.936 47.619 0.00 0.00 0.00 3.86
5401 7248 6.978659 CAGTTCGGAGATTACTTAGTGCATAA 59.021 38.462 0.00 0.00 35.04 1.90
5403 7250 7.491696 AGTTCGGAGATTACTTAGTGCATAAAC 59.508 37.037 0.00 0.00 35.04 2.01
5472 7319 6.042093 TGGCCAAAACATTATTTCTACACCAA 59.958 34.615 0.61 0.00 0.00 3.67
5479 7326 8.519799 AACATTATTTCTACACCAACCATAGG 57.480 34.615 0.00 0.00 0.00 2.57
5484 7331 9.762381 TTATTTCTACACCAACCATAGGAAATT 57.238 29.630 0.00 0.00 0.00 1.82
5485 7332 8.664669 ATTTCTACACCAACCATAGGAAATTT 57.335 30.769 0.00 0.00 0.00 1.82
5486 7333 7.696992 TTCTACACCAACCATAGGAAATTTC 57.303 36.000 9.83 9.83 0.00 2.17
5487 7334 7.027874 TCTACACCAACCATAGGAAATTTCT 57.972 36.000 17.42 6.74 0.00 2.52
5488 7335 5.982890 ACACCAACCATAGGAAATTTCTG 57.017 39.130 17.42 8.32 0.00 3.02
5489 7336 5.640147 ACACCAACCATAGGAAATTTCTGA 58.360 37.500 17.42 6.59 0.00 3.27
5492 7339 5.893824 ACCAACCATAGGAAATTTCTGATCC 59.106 40.000 17.42 1.47 0.00 3.36
5494 7341 6.040166 CCAACCATAGGAAATTTCTGATCCAG 59.960 42.308 17.42 4.37 35.62 3.86
5512 7359 5.552870 TCCAGCTTTCTAGAGAAACTTGT 57.447 39.130 0.46 0.00 38.94 3.16
5626 7473 6.183360 CGTCTTATATTATGGGATGGAGGGAG 60.183 46.154 0.00 0.00 0.00 4.30
5657 7504 8.585471 AGAATTAATTGTGAAGACACCATCAT 57.415 30.769 5.17 0.00 45.40 2.45
5697 7544 4.395231 GGTTGCAAAGTATCTCCCTACAAC 59.605 45.833 0.00 0.00 35.36 3.32
5720 7567 7.787725 ACGTTCTCCTAAAATGGACATTATC 57.212 36.000 0.00 0.00 31.94 1.75
5739 7586 9.382275 ACATTATCAAAAACATTCCTTAATGCC 57.618 29.630 0.00 0.00 45.41 4.40
5742 7589 5.237048 TCAAAAACATTCCTTAATGCCAGC 58.763 37.500 0.00 0.00 45.41 4.85
5743 7590 4.888326 AAAACATTCCTTAATGCCAGCA 57.112 36.364 0.00 0.00 45.41 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 0.037303 ACACACCCTCTTGCTGATGG 59.963 55.000 0.00 0.00 36.66 3.51
8 9 1.821061 CTCCGACACACCCTCTTGCT 61.821 60.000 0.00 0.00 0.00 3.91
58 59 1.352352 CACCACCATCAGACTCCCTTT 59.648 52.381 0.00 0.00 0.00 3.11
60 61 0.117140 TCACCACCATCAGACTCCCT 59.883 55.000 0.00 0.00 0.00 4.20
66 67 1.607801 CGAGCCTCACCACCATCAGA 61.608 60.000 0.00 0.00 0.00 3.27
106 107 3.005539 TGCTCCCCTCTCCTGCAC 61.006 66.667 0.00 0.00 0.00 4.57
107 108 2.686470 CTGCTCCCCTCTCCTGCA 60.686 66.667 0.00 0.00 0.00 4.41
111 112 3.151022 CCGTCTGCTCCCCTCTCC 61.151 72.222 0.00 0.00 0.00 3.71
113 114 3.547787 AACCCGTCTGCTCCCCTCT 62.548 63.158 0.00 0.00 0.00 3.69
123 124 1.415672 TTGCCTTCCAGAACCCGTCT 61.416 55.000 0.00 0.00 36.88 4.18
137 138 3.774144 CCCCCTTTCTCTTTTGCCT 57.226 52.632 0.00 0.00 0.00 4.75
152 153 4.381411 CATAGATTTTCTTCGTCTCCCCC 58.619 47.826 0.00 0.00 0.00 5.40
153 154 4.101119 TCCATAGATTTTCTTCGTCTCCCC 59.899 45.833 0.00 0.00 0.00 4.81
163 164 6.103797 ACAATCCCCATCTCCATAGATTTTCT 59.896 38.462 0.00 0.00 40.65 2.52
221 225 1.284313 TCATGGTCCTATGTGCACCA 58.716 50.000 15.69 2.97 44.36 4.17
229 233 1.202806 CCCACGCATTCATGGTCCTAT 60.203 52.381 0.00 0.00 33.80 2.57
250 254 1.865865 GTCACTTTCCTTCACGCTCA 58.134 50.000 0.00 0.00 0.00 4.26
251 255 0.784778 CGTCACTTTCCTTCACGCTC 59.215 55.000 0.00 0.00 0.00 5.03
256 261 1.939934 CACTTGCGTCACTTTCCTTCA 59.060 47.619 0.00 0.00 0.00 3.02
272 277 1.849976 GCTTGCTCTCTTGCGCACTT 61.850 55.000 11.12 0.00 33.27 3.16
290 295 0.942884 AACTTTCGAACGGTCCGAGC 60.943 55.000 20.51 8.18 37.35 5.03
292 297 3.184094 GAACTTTCGAACGGTCCGA 57.816 52.632 20.51 0.00 0.00 4.55
303 308 1.192534 CGAACAGCTGACCGAACTTTC 59.807 52.381 23.35 9.96 0.00 2.62
304 309 1.202486 TCGAACAGCTGACCGAACTTT 60.202 47.619 23.35 0.26 0.00 2.66
308 313 2.163818 AAATCGAACAGCTGACCGAA 57.836 45.000 28.09 17.17 34.59 4.30
313 318 5.412526 AACGTTTAAAATCGAACAGCTGA 57.587 34.783 23.35 0.00 0.00 4.26
318 323 5.496133 TGGGAAACGTTTAAAATCGAACA 57.504 34.783 14.65 0.00 0.00 3.18
321 326 7.034397 AGTTTTTGGGAAACGTTTAAAATCGA 58.966 30.769 14.65 0.52 35.42 3.59
348 353 9.662947 AAGCTAACTCGTATTTTTAGGTATGTT 57.337 29.630 0.00 0.00 33.50 2.71
352 357 9.793252 CAGTAAGCTAACTCGTATTTTTAGGTA 57.207 33.333 0.00 0.00 33.50 3.08
362 367 1.753073 GGGGCAGTAAGCTAACTCGTA 59.247 52.381 0.00 0.00 44.79 3.43
367 372 2.437085 AATGGGGGCAGTAAGCTAAC 57.563 50.000 0.00 0.00 44.79 2.34
374 379 5.199982 TGATTAAGAAAATGGGGGCAGTA 57.800 39.130 0.00 0.00 0.00 2.74
376 381 5.046376 AGTTTGATTAAGAAAATGGGGGCAG 60.046 40.000 0.00 0.00 0.00 4.85
415 422 3.610040 TTCTTCTTTGCCTATGAGCGA 57.390 42.857 0.00 0.00 34.65 4.93
451 1013 9.987272 TCTCACATGTAAATATAGAATGGACTG 57.013 33.333 0.00 0.00 0.00 3.51
549 1111 2.452813 CCGACGCCTTCCGAATGTG 61.453 63.158 0.00 0.00 41.02 3.21
550 1112 2.125673 CCGACGCCTTCCGAATGT 60.126 61.111 0.00 0.00 41.02 2.71
551 1113 2.125673 ACCGACGCCTTCCGAATG 60.126 61.111 0.00 0.00 41.02 2.67
552 1114 2.125673 CACCGACGCCTTCCGAAT 60.126 61.111 0.00 0.00 41.02 3.34
554 1116 4.351938 CACACCGACGCCTTCCGA 62.352 66.667 0.00 0.00 41.02 4.55
558 1250 0.250124 TCATTTCACACCGACGCCTT 60.250 50.000 0.00 0.00 0.00 4.35
604 1296 3.430218 CGTTTGAGAAACAGCTTCGATCT 59.570 43.478 0.00 0.00 41.44 2.75
613 1305 5.229921 TCTTTTGGTCGTTTGAGAAACAG 57.770 39.130 0.00 0.00 41.44 3.16
614 1306 5.630661 TTCTTTTGGTCGTTTGAGAAACA 57.369 34.783 0.00 0.00 41.44 2.83
746 1445 1.523032 CGAATGGAGGCGGGGTAAC 60.523 63.158 0.00 0.00 0.00 2.50
752 1451 1.666209 ATTTTGGCGAATGGAGGCGG 61.666 55.000 0.00 0.00 36.92 6.13
920 1620 1.993948 GGGGAGGAACTAAGCGGGT 60.994 63.158 0.00 0.00 41.55 5.28
926 1626 2.910977 GAGGAAGTTGGGGAGGAACTAA 59.089 50.000 0.00 0.00 41.55 2.24
927 1627 2.547990 GAGGAAGTTGGGGAGGAACTA 58.452 52.381 0.00 0.00 41.55 2.24
943 1643 1.916181 GTGGAGGGAGAATTTGGAGGA 59.084 52.381 0.00 0.00 0.00 3.71
1195 1895 2.658422 GGAACTTACGTGGCCGGA 59.342 61.111 5.05 0.00 38.78 5.14
1201 1901 2.435410 GGGCGGGGAACTTACGTG 60.435 66.667 0.00 0.00 0.00 4.49
1203 1903 4.478371 GGGGGCGGGGAACTTACG 62.478 72.222 0.00 0.00 0.00 3.18
1262 2294 1.730501 CGCACATTGTCAGGAGATGT 58.269 50.000 0.00 0.00 34.52 3.06
1281 2313 2.970974 GCAAGGTCGAGCAGTTGGC 61.971 63.158 18.15 8.62 45.30 4.52
1648 2680 1.968493 GACAGTGTCTTCCCTGTACCA 59.032 52.381 16.26 0.00 41.80 3.25
1722 2754 7.945134 AGAAAATTGCTCACATACTGAAAACT 58.055 30.769 0.00 0.00 0.00 2.66
1724 2756 8.077991 CAGAGAAAATTGCTCACATACTGAAAA 58.922 33.333 3.48 0.00 34.85 2.29
1742 2774 6.850752 AGTTCCCTTTTGAAACAGAGAAAA 57.149 33.333 0.00 0.00 0.00 2.29
1761 2793 4.904116 TGACACACGATTTGACAAAGTTC 58.096 39.130 6.77 0.00 0.00 3.01
1775 2807 1.662360 CGCAAGACAAATGACACACG 58.338 50.000 0.00 0.00 43.02 4.49
1791 2823 1.227527 CCATTCCCATCTACGCGCA 60.228 57.895 5.73 0.00 0.00 6.09
1841 2873 3.631686 TGTCAGATGTGTTTCCAAGGTTG 59.368 43.478 0.00 0.00 0.00 3.77
1885 2917 7.047460 AGATTTGAGCCCATAATTTTAGCAG 57.953 36.000 0.00 0.00 0.00 4.24
1918 2950 0.465705 TGATCGATCAGCTTGGGGAC 59.534 55.000 23.99 0.00 32.11 4.46
1919 2951 1.071228 CATGATCGATCAGCTTGGGGA 59.929 52.381 30.11 6.50 40.64 4.81
1952 2984 6.983474 TTTCGAGTATCTGCATTGAAATCA 57.017 33.333 0.00 0.00 0.00 2.57
1971 3003 3.907894 TTCCGAACCTGGAATTTTTCG 57.092 42.857 0.00 4.99 43.01 3.46
2129 3162 5.400782 GCGATGACATACAGTTCAGATAGTG 59.599 44.000 0.00 0.00 0.00 2.74
2130 3163 5.300539 AGCGATGACATACAGTTCAGATAGT 59.699 40.000 0.00 0.00 0.00 2.12
2150 3183 0.537143 ACAACCAATCTGGCAAGCGA 60.537 50.000 0.00 0.00 42.67 4.93
2167 3200 4.096681 AGTAGTCCATCTCATCCACAACA 58.903 43.478 0.00 0.00 0.00 3.33
2282 3315 6.659745 AGTGTACATTGTAGGTGTGAGTAA 57.340 37.500 0.00 0.00 0.00 2.24
2404 3439 3.633065 AGAAACCGATCTGCTAGGTCTAC 59.367 47.826 0.00 0.00 37.26 2.59
2476 3511 4.588106 TGAAGGAGCCATTCAATTTTCACA 59.412 37.500 0.69 0.00 33.85 3.58
2962 4688 1.521681 GCGCCTACCCTCACATCAC 60.522 63.158 0.00 0.00 0.00 3.06
2995 4721 0.906066 TAGCTTACGATTGGGTGCCA 59.094 50.000 0.00 0.00 0.00 4.92
2997 4723 5.744666 TTATTTAGCTTACGATTGGGTGC 57.255 39.130 0.00 0.00 0.00 5.01
3070 4796 5.621193 ACACTTACAGGCACAAATACTTCT 58.379 37.500 0.00 0.00 0.00 2.85
3086 4812 5.681639 ACCATATCCCTTAGCAACACTTAC 58.318 41.667 0.00 0.00 0.00 2.34
3134 4864 4.697352 GCTGAGATGTACACACCAGATTTT 59.303 41.667 18.70 0.00 0.00 1.82
3175 4913 1.597302 CGGAGCATCAGCATCCCTG 60.597 63.158 0.00 0.00 45.49 4.45
3383 5121 7.478322 CCATATCCAGAACTCTTTCAACAATG 58.522 38.462 0.00 0.00 33.72 2.82
3409 5147 8.607441 TTCAATAAGCTATACATAAGCACCAG 57.393 34.615 0.00 0.00 42.62 4.00
3514 5252 3.253432 CCAAGAAACTTACAACTCCAGCC 59.747 47.826 0.00 0.00 0.00 4.85
3581 5319 5.105064 GGCTTGGTGTAGAGACCACTTTATA 60.105 44.000 0.00 0.00 46.03 0.98
3635 5373 6.071952 ACAGATGAACTAATGGCAAAAATCGT 60.072 34.615 0.00 0.00 0.00 3.73
3636 5374 6.324819 ACAGATGAACTAATGGCAAAAATCG 58.675 36.000 0.00 0.00 0.00 3.34
3759 5497 2.373502 GGGAATTGGGAGGATAGACAGG 59.626 54.545 0.00 0.00 0.00 4.00
3799 5537 5.435686 AGCCTAGTAATGGATGTTGTTCA 57.564 39.130 0.00 0.00 0.00 3.18
3867 5605 9.807921 AGAATCCTCTCAAAAAGGTAATTTGTA 57.192 29.630 0.00 0.00 38.57 2.41
3870 5608 9.807921 TGTAGAATCCTCTCAAAAAGGTAATTT 57.192 29.630 0.00 0.00 35.29 1.82
3888 5627 8.430801 AAGCATGTTATCTGTTCTGTAGAATC 57.569 34.615 0.00 0.00 36.33 2.52
3891 5630 7.361201 GCAAAAGCATGTTATCTGTTCTGTAGA 60.361 37.037 0.00 0.00 0.00 2.59
3904 5643 3.636300 AGGAACACAGCAAAAGCATGTTA 59.364 39.130 9.22 0.00 0.00 2.41
3913 5652 4.350368 TCAGATACAGGAACACAGCAAA 57.650 40.909 0.00 0.00 0.00 3.68
3915 5654 5.876651 ATATCAGATACAGGAACACAGCA 57.123 39.130 0.00 0.00 0.00 4.41
3974 5715 8.138712 GGGTGTAAGAAGAGATAACACTCTATG 58.861 40.741 0.00 0.00 45.08 2.23
3980 5721 5.176592 GTGGGGTGTAAGAAGAGATAACAC 58.823 45.833 0.00 0.00 39.72 3.32
3996 5817 1.898902 TAACATTGGAACGTGGGGTG 58.101 50.000 0.00 0.00 0.00 4.61
4004 5825 7.312154 TGTTAGATTGCACATAACATTGGAAC 58.688 34.615 11.58 0.00 35.17 3.62
4054 5875 3.118445 TCGACAAGGCAATGTCCATATGA 60.118 43.478 15.12 6.07 45.51 2.15
4679 6504 4.142513 GGTGTAGTTACAGGAGTAAGACCG 60.143 50.000 0.00 0.00 40.68 4.79
4687 6512 6.873997 TGACATATTGGTGTAGTTACAGGAG 58.126 40.000 0.00 0.00 36.78 3.69
4689 6514 5.523916 GCTGACATATTGGTGTAGTTACAGG 59.476 44.000 0.00 0.00 36.78 4.00
4810 6635 8.743714 CACTTAAAGAAAATCCTAGGAAGCATT 58.256 33.333 17.30 8.42 0.00 3.56
4935 6763 8.970859 AAGACTGAATTGGTAAGGAATCTATG 57.029 34.615 0.00 0.00 0.00 2.23
4982 6810 6.591062 GGAAAAAGCTTGATACAATGAATGCA 59.409 34.615 0.00 0.00 0.00 3.96
4983 6811 6.237648 CGGAAAAAGCTTGATACAATGAATGC 60.238 38.462 0.00 0.00 0.00 3.56
5007 6840 0.240145 TAACCAGCAGACGACTGACG 59.760 55.000 19.07 7.91 46.03 4.35
5315 7153 2.091994 AGATGAAAGGCCATTCCTCAGG 60.092 50.000 22.59 0.00 46.94 3.86
5326 7164 4.836125 TGAGACAAACAAGATGAAAGGC 57.164 40.909 0.00 0.00 0.00 4.35
5328 7166 5.824429 TGCTTGAGACAAACAAGATGAAAG 58.176 37.500 11.08 0.00 44.92 2.62
5362 7200 2.744202 CCGAACTGGATTTGGAGTCAAG 59.256 50.000 0.00 0.00 44.08 3.02
5364 7202 1.974957 TCCGAACTGGATTTGGAGTCA 59.025 47.619 0.00 0.00 44.87 3.41
5378 7225 7.514747 CGTTTATGCACTAAGTAATCTCCGAAC 60.515 40.741 0.00 0.00 0.00 3.95
5401 7248 6.482308 GGTAGTATGCCATAAAGTTGATCGTT 59.518 38.462 0.00 0.00 42.29 3.85
5403 7250 5.408604 GGGTAGTATGCCATAAAGTTGATCG 59.591 44.000 0.00 0.00 45.88 3.69
5472 7319 5.103771 AGCTGGATCAGAAATTTCCTATGGT 60.104 40.000 14.61 3.01 32.44 3.55
5478 7325 5.911378 AGAAAGCTGGATCAGAAATTTCC 57.089 39.130 14.61 0.11 34.05 3.13
5479 7326 7.768120 TCTCTAGAAAGCTGGATCAGAAATTTC 59.232 37.037 10.33 10.33 33.90 2.17
5484 7331 6.212388 AGTTTCTCTAGAAAGCTGGATCAGAA 59.788 38.462 5.41 0.00 43.82 3.02
5485 7332 5.719085 AGTTTCTCTAGAAAGCTGGATCAGA 59.281 40.000 5.41 0.00 43.82 3.27
5486 7333 5.976458 AGTTTCTCTAGAAAGCTGGATCAG 58.024 41.667 5.41 0.00 43.82 2.90
5487 7334 6.169094 CAAGTTTCTCTAGAAAGCTGGATCA 58.831 40.000 5.41 0.00 43.82 2.92
5488 7335 6.091986 CACAAGTTTCTCTAGAAAGCTGGATC 59.908 42.308 5.41 0.00 43.82 3.36
5489 7336 5.936956 CACAAGTTTCTCTAGAAAGCTGGAT 59.063 40.000 5.41 0.00 43.82 3.41
5492 7339 6.851222 TTCACAAGTTTCTCTAGAAAGCTG 57.149 37.500 5.41 8.31 43.82 4.24
5586 7433 8.669394 AATATAAGACGTTTTTGCAAGCTAAC 57.331 30.769 0.00 5.28 0.00 2.34
5602 7449 6.674419 ACTCCCTCCATCCCATAATATAAGAC 59.326 42.308 0.00 0.00 0.00 3.01
5657 7504 6.154203 TGCAACCAGAAAATCATTAACACA 57.846 33.333 0.00 0.00 0.00 3.72
5664 7511 7.363268 GGAGATACTTTGCAACCAGAAAATCAT 60.363 37.037 0.00 0.00 0.00 2.45
5697 7544 7.786178 TGATAATGTCCATTTTAGGAGAACG 57.214 36.000 0.00 0.00 38.64 3.95
5720 7567 4.996122 TGCTGGCATTAAGGAATGTTTTTG 59.004 37.500 0.00 0.00 43.82 2.44


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

AutoCloner maintained by Alex Coulton.