Multiple sequence alignment - TraesCS6A01G004700

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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 TraesCS6A01G004700 chr6A 100.000 5528 0 0 1 5528 1893139 1898666 0.000000e+00 10209.0
1 TraesCS6A01G004700 chr6A 77.512 2170 404 58 2379 4497 1921932 1924068 0.000000e+00 1227.0
2 TraesCS6A01G004700 chr6A 95.652 46 2 0 385 430 73561992 73562037 2.140000e-09 75.0
3 TraesCS6A01G004700 chr6A 93.750 48 3 0 383 430 480647887 480647934 7.680000e-09 73.1
4 TraesCS6A01G004700 chr6D 93.533 3912 201 21 651 4544 2910169 2914046 0.000000e+00 5775.0
5 TraesCS6A01G004700 chr6D 79.260 2107 391 29 2405 4494 3076590 3074513 0.000000e+00 1428.0
6 TraesCS6A01G004700 chr6D 89.558 1063 73 16 193 1235 2894496 2895540 0.000000e+00 1314.0
7 TraesCS6A01G004700 chr6D 78.597 1696 325 29 2941 4621 2897110 2898782 0.000000e+00 1086.0
8 TraesCS6A01G004700 chr6D 82.833 466 68 9 2405 2869 2896557 2897011 1.850000e-109 407.0
9 TraesCS6A01G004700 chr6D 79.895 572 64 16 1608 2139 2895983 2896543 6.760000e-99 372.0
10 TraesCS6A01G004700 chr6D 86.269 335 20 10 4627 4956 2914054 2914367 1.910000e-89 340.0
11 TraesCS6A01G004700 chr6D 82.927 410 34 16 5089 5477 2914719 2915113 2.470000e-88 337.0
12 TraesCS6A01G004700 chr6D 87.603 242 30 0 1900 2141 3076843 3076602 1.170000e-71 281.0
13 TraesCS6A01G004700 chr6D 89.623 212 9 4 1 199 2894241 2894452 1.980000e-64 257.0
14 TraesCS6A01G004700 chr6D 87.500 152 18 1 3722 3872 2923222 2923373 2.050000e-39 174.0
15 TraesCS6A01G004700 chr6D 95.652 46 2 0 385 430 58245375 58245420 2.140000e-09 75.0
16 TraesCS6A01G004700 chr6B 93.386 3432 181 19 1485 4887 6023608 6027022 0.000000e+00 5038.0
17 TraesCS6A01G004700 chr6B 91.979 748 52 5 493 1237 6022623 6023365 0.000000e+00 1042.0
18 TraesCS6A01G004700 chr6B 91.391 604 22 11 4884 5462 6027075 6027673 0.000000e+00 800.0
19 TraesCS6A01G004700 chr6B 79.397 597 111 8 2405 2995 6240552 6239962 1.430000e-110 411.0
20 TraesCS6A01G004700 chr6B 88.017 242 29 0 1900 2141 6240805 6240564 2.520000e-73 287.0
21 TraesCS6A01G004700 chr6B 76.726 507 108 7 2382 2883 6271644 6271143 1.960000e-69 274.0
22 TraesCS6A01G004700 chr6B 86.383 235 17 10 193 417 6022398 6022627 5.530000e-60 243.0
23 TraesCS6A01G004700 chr1D 95.745 47 2 0 384 430 225414286 225414240 5.940000e-10 76.8
24 TraesCS6A01G004700 chr1A 94.118 51 1 2 381 430 292767902 292767951 5.940000e-10 76.8
25 TraesCS6A01G004700 chr1A 100.000 30 0 0 1440 1469 105322621 105322650 7.740000e-04 56.5
26 TraesCS6A01G004700 chr1B 93.617 47 3 0 384 430 325271810 325271764 2.760000e-08 71.3
27 TraesCS6A01G004700 chr5D 82.927 82 9 3 385 462 387683649 387683569 9.940000e-08 69.4
28 TraesCS6A01G004700 chr7B 93.333 45 2 1 1442 1486 156303743 156303786 1.290000e-06 65.8
29 TraesCS6A01G004700 chr3D 93.333 45 2 1 1442 1486 151235106 151235149 1.290000e-06 65.8


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 TraesCS6A01G004700 chr6A 1893139 1898666 5527 False 10209.000000 10209 100.000000 1 5528 1 chr6A.!!$F1 5527
1 TraesCS6A01G004700 chr6A 1921932 1924068 2136 False 1227.000000 1227 77.512000 2379 4497 1 chr6A.!!$F2 2118
2 TraesCS6A01G004700 chr6D 2910169 2915113 4944 False 2150.666667 5775 87.576333 651 5477 3 chr6D.!!$F4 4826
3 TraesCS6A01G004700 chr6D 3074513 3076843 2330 True 854.500000 1428 83.431500 1900 4494 2 chr6D.!!$R1 2594
4 TraesCS6A01G004700 chr6D 2894241 2898782 4541 False 687.200000 1314 84.101200 1 4621 5 chr6D.!!$F3 4620
5 TraesCS6A01G004700 chr6B 6022398 6027673 5275 False 1780.750000 5038 90.784750 193 5462 4 chr6B.!!$F1 5269
6 TraesCS6A01G004700 chr6B 6239962 6240805 843 True 349.000000 411 83.707000 1900 2995 2 chr6B.!!$R2 1095
7 TraesCS6A01G004700 chr6B 6271143 6271644 501 True 274.000000 274 76.726000 2382 2883 1 chr6B.!!$R1 501

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
267 344 0.512952 GCCGTGAGTGTGTCAATGAC 59.487 55.0 6.41 6.41 36.74 3.06 F
1258 1445 0.375803 GCACACGTTCGGTCTTTGTT 59.624 50.0 0.00 0.00 0.00 2.83 F
1608 1891 1.127343 AGTGCCTAGGAATCCAGCTC 58.873 55.0 14.75 2.62 0.00 4.09 F
3072 3478 0.250038 TCGCACTCTTCAAGCTGCTT 60.250 50.0 9.53 9.53 32.90 3.91 F
3713 4119 1.022735 CAGATCACCATGCTCAAGCC 58.977 55.0 0.00 0.00 41.18 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1650 1957 0.591659 CAAGGCATGGATCGATGCTG 59.408 55.0 32.85 23.68 46.74 4.41 R
2770 3140 0.249280 ACTGCGTGTTCGTCATCACA 60.249 50.0 0.00 0.00 39.49 3.58 R
3228 3634 0.330604 TGGCCTGGTAGTACTCGTCT 59.669 55.0 3.32 0.00 0.00 4.18 R
4228 4637 0.321564 TTCACCATGGCCGACTTCTG 60.322 55.0 13.04 0.00 0.00 3.02 R
5477 6253 0.179097 GGACGCCAAGAGCTAAGAGG 60.179 60.0 0.00 0.00 40.39 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
99 113 9.997482 AAACGCCTTACATTAACATATAAGTTG 57.003 29.630 3.63 0.00 33.07 3.16
115 129 4.574599 AAGTTGTTCAGGTTGATCAAGC 57.425 40.909 26.43 26.43 36.93 4.01
127 141 7.552687 TCAGGTTGATCAAGCGTAAAATAGATT 59.447 33.333 27.00 6.85 43.06 2.40
178 192 3.064900 AGATGAAAGGAAGGAGTGTGC 57.935 47.619 0.00 0.00 0.00 4.57
216 280 1.902508 TGTTCTTCCTGGCCTCTACTG 59.097 52.381 3.32 0.00 0.00 2.74
264 341 1.667830 CCGCCGTGAGTGTGTCAAT 60.668 57.895 0.00 0.00 36.74 2.57
265 342 1.492873 CGCCGTGAGTGTGTCAATG 59.507 57.895 0.00 0.00 36.74 2.82
266 343 0.943835 CGCCGTGAGTGTGTCAATGA 60.944 55.000 0.00 0.00 36.74 2.57
267 344 0.512952 GCCGTGAGTGTGTCAATGAC 59.487 55.000 6.41 6.41 36.74 3.06
268 345 1.864565 CCGTGAGTGTGTCAATGACA 58.135 50.000 12.63 12.63 40.50 3.58
269 346 2.416747 CCGTGAGTGTGTCAATGACAT 58.583 47.619 19.72 3.27 44.63 3.06
270 347 2.807967 CCGTGAGTGTGTCAATGACATT 59.192 45.455 19.72 8.40 44.63 2.71
271 348 3.120546 CCGTGAGTGTGTCAATGACATTC 60.121 47.826 19.72 16.46 44.63 2.67
272 349 3.742882 CGTGAGTGTGTCAATGACATTCT 59.257 43.478 19.72 18.62 44.63 2.40
312 389 0.541392 TGATGGCTACACGAATGCCT 59.459 50.000 12.64 1.96 46.23 4.75
313 390 1.065491 TGATGGCTACACGAATGCCTT 60.065 47.619 12.64 7.85 46.23 4.35
620 700 9.661187 CATACTTGAGCTAGCATTTTCAAATAG 57.339 33.333 18.83 8.63 0.00 1.73
622 702 8.792830 ACTTGAGCTAGCATTTTCAAATAGTA 57.207 30.769 18.83 0.00 0.00 1.82
623 703 9.401058 ACTTGAGCTAGCATTTTCAAATAGTAT 57.599 29.630 18.83 0.00 0.00 2.12
624 704 9.661187 CTTGAGCTAGCATTTTCAAATAGTATG 57.339 33.333 18.83 0.98 0.00 2.39
704 784 3.443588 GCCCAAACAAACGAGGCT 58.556 55.556 0.00 0.00 40.57 4.58
728 809 7.381139 GCTCAAGTATGCTAGAAGCTAACTTAG 59.619 40.741 14.67 13.34 41.49 2.18
753 842 2.490991 AGCGAAAGGTAAAGAAGCGTT 58.509 42.857 0.00 0.00 41.99 4.84
761 850 3.579151 AGGTAAAGAAGCGTTCTCTTCCT 59.421 43.478 0.41 6.36 42.52 3.36
777 866 5.073144 TCTCTTCCTGGTTATCCTTTTGTGT 59.927 40.000 0.00 0.00 34.23 3.72
780 869 5.255397 TCCTGGTTATCCTTTTGTGTGAT 57.745 39.130 0.00 0.00 34.23 3.06
792 881 6.998074 TCCTTTTGTGTGATATGTTCTTCTGT 59.002 34.615 0.00 0.00 0.00 3.41
882 971 8.484214 TCTGAGAATATATAAAGACCTGCTGT 57.516 34.615 0.00 0.00 0.00 4.40
897 986 0.531974 GCTGTGTTCTTGGTCGTGGA 60.532 55.000 0.00 0.00 0.00 4.02
900 989 0.586802 GTGTTCTTGGTCGTGGAAGC 59.413 55.000 0.00 0.00 0.00 3.86
949 1040 1.153168 GCGCATGTATGTCCCAGGT 60.153 57.895 0.30 0.00 0.00 4.00
1025 1117 3.066760 CACACCCTCAAACCAGAGAAAAC 59.933 47.826 0.00 0.00 37.87 2.43
1060 1152 4.982241 TCCCAGGTGATTCTAATGATCC 57.018 45.455 0.00 0.00 0.00 3.36
1063 1155 5.433051 TCCCAGGTGATTCTAATGATCCTTT 59.567 40.000 0.00 0.00 0.00 3.11
1138 1246 5.698741 ACTGTATGATGATGAACCTTCCA 57.301 39.130 0.00 0.00 0.00 3.53
1143 1251 8.681486 TGTATGATGATGAACCTTCCAATTAG 57.319 34.615 0.00 0.00 0.00 1.73
1177 1285 3.731652 TGTGCCTTTGTTTTCCATGAG 57.268 42.857 0.00 0.00 0.00 2.90
1186 1294 3.696045 TGTTTTCCATGAGGTATGTGGG 58.304 45.455 0.00 0.00 34.87 4.61
1241 1425 1.061546 AACCGAAACCTTAGAGGGCA 58.938 50.000 0.00 0.00 40.58 5.36
1258 1445 0.375803 GCACACGTTCGGTCTTTGTT 59.624 50.000 0.00 0.00 0.00 2.83
1297 1501 4.534103 ACCTCAGCCTTCTCATAAGAAACT 59.466 41.667 0.00 0.00 40.95 2.66
1299 1503 5.337894 CCTCAGCCTTCTCATAAGAAACTGA 60.338 44.000 9.57 9.57 44.51 3.41
1300 1504 5.728471 TCAGCCTTCTCATAAGAAACTGAG 58.272 41.667 6.83 0.00 43.26 3.35
1313 1517 5.508200 AGAAACTGAGACGAGCCTATTAG 57.492 43.478 0.00 0.00 0.00 1.73
1356 1560 7.362920 GGGCAATATGTACAAGAAGTCACATTT 60.363 37.037 0.00 0.00 33.78 2.32
1399 1603 3.262448 TACAAGCCCCAAGACCGCC 62.262 63.158 0.00 0.00 0.00 6.13
1419 1697 4.183865 GCCTGTTTTGAAATAGGGCATTC 58.816 43.478 17.47 1.33 44.64 2.67
1432 1710 1.407979 GGGCATTCTCAAAGCAGGATG 59.592 52.381 0.00 0.00 40.87 3.51
1466 1744 6.037098 ACATAGCTTGCAAAAACGTTTTACA 58.963 32.000 25.44 22.17 0.00 2.41
1472 1750 5.456192 TGCAAAAACGTTTTACATTGTGG 57.544 34.783 25.44 9.59 0.00 4.17
1476 1754 4.985538 AAACGTTTTACATTGTGGGACA 57.014 36.364 7.96 0.00 0.00 4.02
1499 1777 8.840200 ACAGAGGGAGTAGTTCTCAAAATATA 57.160 34.615 0.00 0.00 44.40 0.86
1501 1779 9.757227 CAGAGGGAGTAGTTCTCAAAATATAAG 57.243 37.037 0.00 0.00 44.40 1.73
1502 1780 9.495382 AGAGGGAGTAGTTCTCAAAATATAAGT 57.505 33.333 0.00 0.00 44.40 2.24
1503 1781 9.752961 GAGGGAGTAGTTCTCAAAATATAAGTC 57.247 37.037 0.00 0.00 44.40 3.01
1603 1886 2.119495 TGGAGAAGTGCCTAGGAATCC 58.881 52.381 14.75 6.56 0.00 3.01
1607 1890 1.488393 GAAGTGCCTAGGAATCCAGCT 59.512 52.381 14.75 0.00 0.00 4.24
1608 1891 1.127343 AGTGCCTAGGAATCCAGCTC 58.873 55.000 14.75 2.62 0.00 4.09
1618 1925 2.641305 GAATCCAGCTCAAGCAGATGT 58.359 47.619 4.59 0.00 45.16 3.06
1676 1983 1.202687 CGATCCATGCCTTGCCTCTTA 60.203 52.381 0.00 0.00 0.00 2.10
1725 2034 1.550659 GCACACGCATGCCAAAACTG 61.551 55.000 13.15 0.00 39.86 3.16
1749 2058 6.490381 TGGCAGTACAAATACCACAAACATAA 59.510 34.615 0.00 0.00 30.88 1.90
1750 2059 7.027161 GGCAGTACAAATACCACAAACATAAG 58.973 38.462 0.00 0.00 30.88 1.73
1869 2229 4.752879 TACAACTCCAGCGCCCGC 62.753 66.667 2.29 4.20 42.33 6.13
1890 2250 2.288729 CCGCGACATCATCATCAACAAT 59.711 45.455 8.23 0.00 0.00 2.71
1962 2323 3.550992 GCCGACATGCGTACCACG 61.551 66.667 8.37 0.00 45.88 4.94
1983 2344 2.347114 CGGCTCATGGTCACCACA 59.653 61.111 0.00 0.00 35.80 4.17
2082 2443 2.442458 TCTACCGCCACCCGCATA 60.442 61.111 0.00 0.00 37.30 3.14
2109 2470 1.216710 CGCCTCCTTCGCTCTCTTT 59.783 57.895 0.00 0.00 0.00 2.52
2321 2691 8.721019 ATTTTGAGGTTGCATATATTTTGGTG 57.279 30.769 0.00 0.00 0.00 4.17
2770 3140 1.672356 AAGCGTCGGCAATTGCTCT 60.672 52.632 28.42 14.97 43.41 4.09
2802 3181 2.202960 GCAGTTGGCGCCGGTATA 60.203 61.111 23.90 0.00 0.00 1.47
2892 3271 7.249858 GCTTCAAGATCCAAGAAGAAGAAATC 58.750 38.462 18.33 1.54 40.85 2.17
2939 3345 2.358258 TCCAAATGGGAAGGAAGAGGT 58.642 47.619 0.00 0.00 44.80 3.85
3018 3424 6.129179 CCCCATATTCAGGTACAATTTGAGT 58.871 40.000 2.79 0.00 0.00 3.41
3072 3478 0.250038 TCGCACTCTTCAAGCTGCTT 60.250 50.000 9.53 9.53 32.90 3.91
3108 3514 2.046023 TTCCACATGGCAGAGGCG 60.046 61.111 0.00 0.00 42.47 5.52
3144 3550 2.195139 GATCTCGTCCTCCGGGGA 59.805 66.667 0.37 4.95 42.77 4.81
3228 3634 2.567615 GGAACTGGAGCTGAGGTTTCTA 59.432 50.000 0.00 0.00 0.00 2.10
3438 3844 1.676006 GTGGTGCAGTACAAGTGCTTT 59.324 47.619 8.11 0.00 44.61 3.51
3579 3985 3.996363 TCTCTGATTGGTTCATTGTGTCG 59.004 43.478 0.00 0.00 32.72 4.35
3713 4119 1.022735 CAGATCACCATGCTCAAGCC 58.977 55.000 0.00 0.00 41.18 4.35
3815 4221 1.525077 TCACCGGTGACACAAAGGC 60.525 57.895 33.23 0.00 34.14 4.35
3924 4330 1.440618 TCCTTAACCTCAAGTGGGCA 58.559 50.000 0.00 0.00 0.00 5.36
4228 4637 1.135228 GTCAAGGAGAAGAGGACGAGC 60.135 57.143 0.00 0.00 0.00 5.03
4488 4921 0.112412 ATGTCCCCAAGAACCACCAC 59.888 55.000 0.00 0.00 0.00 4.16
4520 4953 1.028330 CCATCGTGCAACTGCCATCT 61.028 55.000 0.00 0.00 41.18 2.90
4567 5000 0.545171 CCCATCACAGCCAGTCTCAT 59.455 55.000 0.00 0.00 0.00 2.90
4575 5008 4.008330 CACAGCCAGTCTCATCAAATTCT 58.992 43.478 0.00 0.00 0.00 2.40
4579 5012 5.048224 CAGCCAGTCTCATCAAATTCTTTGT 60.048 40.000 0.04 0.00 41.36 2.83
4606 5039 9.567848 TTATTTGTTGTTGTTTTGAGAAGAGTC 57.432 29.630 0.00 0.00 0.00 3.36
4683 5118 9.764363 TCTGATTTATACAAGTATTAGCTGGTG 57.236 33.333 0.00 0.00 0.00 4.17
4742 5179 8.743085 AATCATGTAATGTTCTAGCACAAGAT 57.257 30.769 0.00 0.00 46.80 2.40
4746 5183 5.582269 TGTAATGTTCTAGCACAAGATGAGC 59.418 40.000 0.00 0.00 34.10 4.26
4768 5205 2.294512 TGAGATGGCATAGCTACACTCG 59.705 50.000 0.00 0.00 32.30 4.18
4791 5228 1.068748 CCAGTTGTGCTTGCAGATGAC 60.069 52.381 0.00 0.00 0.00 3.06
4793 5230 3.069289 CAGTTGTGCTTGCAGATGACTA 58.931 45.455 0.00 0.00 0.00 2.59
4797 5234 6.703165 CAGTTGTGCTTGCAGATGACTATATA 59.297 38.462 0.00 0.00 0.00 0.86
4798 5235 7.387122 CAGTTGTGCTTGCAGATGACTATATAT 59.613 37.037 0.00 0.00 0.00 0.86
4799 5236 7.601886 AGTTGTGCTTGCAGATGACTATATATC 59.398 37.037 0.00 0.00 0.00 1.63
4800 5237 6.095377 TGTGCTTGCAGATGACTATATATCG 58.905 40.000 0.00 0.00 0.00 2.92
4841 5278 6.704937 TGATCTTGATGCAGACATAGTGATTC 59.295 38.462 0.00 0.00 36.35 2.52
4845 5282 8.260114 TCTTGATGCAGACATAGTGATTCTTAA 58.740 33.333 0.00 0.00 36.35 1.85
4846 5283 8.969260 TTGATGCAGACATAGTGATTCTTAAT 57.031 30.769 0.00 0.00 36.35 1.40
4848 5285 9.399797 TGATGCAGACATAGTGATTCTTAATTT 57.600 29.630 0.00 0.00 36.35 1.82
4850 5287 8.791327 TGCAGACATAGTGATTCTTAATTTGA 57.209 30.769 0.00 0.00 0.00 2.69
4851 5288 9.399797 TGCAGACATAGTGATTCTTAATTTGAT 57.600 29.630 0.00 0.00 0.00 2.57
4852 5289 9.661187 GCAGACATAGTGATTCTTAATTTGATG 57.339 33.333 0.00 0.00 0.00 3.07
4995 5528 3.118884 CCCAGCAAGCAAAGCTATTCATT 60.119 43.478 0.00 0.00 41.14 2.57
5018 5703 6.560003 TTTAATCTTGATGTAGCAGGAGGA 57.440 37.500 0.00 0.00 0.00 3.71
5036 5721 6.023603 AGGAGGATACCCGTCATATGTAATT 58.976 40.000 1.90 0.00 37.58 1.40
5037 5722 7.123697 CAGGAGGATACCCGTCATATGTAATTA 59.876 40.741 1.90 0.00 37.58 1.40
5038 5723 7.676893 AGGAGGATACCCGTCATATGTAATTAA 59.323 37.037 1.90 0.00 37.58 1.40
5039 5724 8.483758 GGAGGATACCCGTCATATGTAATTAAT 58.516 37.037 1.90 0.00 37.58 1.40
5070 5755 2.517650 TTTCAAATCACGGTTTGGGC 57.482 45.000 3.07 0.00 39.10 5.36
5207 5954 2.767505 GAAACGAGTGGTGATGGAGTT 58.232 47.619 0.00 0.00 0.00 3.01
5209 5956 0.321671 ACGAGTGGTGATGGAGTTGG 59.678 55.000 0.00 0.00 0.00 3.77
5477 6253 3.890527 ATGGAGAACATGGGCTCAC 57.109 52.632 15.97 8.27 38.70 3.51
5478 6254 0.257039 ATGGAGAACATGGGCTCACC 59.743 55.000 15.97 9.37 38.70 4.02
5479 6255 0.842030 TGGAGAACATGGGCTCACCT 60.842 55.000 15.97 0.00 41.11 4.00
5480 6256 0.107459 GGAGAACATGGGCTCACCTC 60.107 60.000 15.97 0.00 41.11 3.85
5481 6257 0.908198 GAGAACATGGGCTCACCTCT 59.092 55.000 11.00 0.00 41.11 3.69
5482 6258 1.280421 GAGAACATGGGCTCACCTCTT 59.720 52.381 11.00 0.00 41.11 2.85
5483 6259 2.501723 GAGAACATGGGCTCACCTCTTA 59.498 50.000 11.00 0.00 41.11 2.10
5484 6260 2.503356 AGAACATGGGCTCACCTCTTAG 59.497 50.000 0.00 0.00 41.11 2.18
5485 6261 0.543749 ACATGGGCTCACCTCTTAGC 59.456 55.000 0.00 0.00 41.11 3.09
5486 6262 0.835941 CATGGGCTCACCTCTTAGCT 59.164 55.000 0.00 0.00 41.11 3.32
5487 6263 1.127343 ATGGGCTCACCTCTTAGCTC 58.873 55.000 0.00 0.00 39.78 4.09
5488 6264 0.041833 TGGGCTCACCTCTTAGCTCT 59.958 55.000 0.00 0.00 40.05 4.09
5489 6265 1.199615 GGGCTCACCTCTTAGCTCTT 58.800 55.000 0.00 0.00 36.24 2.85
5490 6266 1.134551 GGGCTCACCTCTTAGCTCTTG 60.135 57.143 0.00 0.00 36.24 3.02
5491 6267 1.134551 GGCTCACCTCTTAGCTCTTGG 60.135 57.143 0.00 0.00 38.80 3.61
5492 6268 1.742071 GCTCACCTCTTAGCTCTTGGC 60.742 57.143 0.00 0.00 42.19 4.52
5501 6277 2.435059 GCTCTTGGCGTCCAGACC 60.435 66.667 0.00 0.00 33.81 3.85
5502 6278 2.948720 GCTCTTGGCGTCCAGACCT 61.949 63.158 0.00 0.00 33.81 3.85
5503 6279 1.674057 CTCTTGGCGTCCAGACCTT 59.326 57.895 0.00 0.00 33.81 3.50
5504 6280 0.390472 CTCTTGGCGTCCAGACCTTC 60.390 60.000 0.00 0.00 33.81 3.46
5505 6281 1.376037 CTTGGCGTCCAGACCTTCC 60.376 63.158 0.00 0.00 33.81 3.46
5506 6282 3.234630 TTGGCGTCCAGACCTTCCG 62.235 63.158 0.00 0.00 33.81 4.30
5507 6283 3.692406 GGCGTCCAGACCTTCCGT 61.692 66.667 0.00 0.00 0.00 4.69
5508 6284 2.126031 GCGTCCAGACCTTCCGTC 60.126 66.667 0.00 0.00 42.32 4.79
5509 6285 2.178521 CGTCCAGACCTTCCGTCG 59.821 66.667 0.00 0.00 46.92 5.12
5510 6286 2.330372 CGTCCAGACCTTCCGTCGA 61.330 63.158 0.00 0.00 46.92 4.20
5511 6287 1.859427 CGTCCAGACCTTCCGTCGAA 61.859 60.000 0.00 0.00 46.92 3.71
5512 6288 0.388263 GTCCAGACCTTCCGTCGAAC 60.388 60.000 0.00 0.00 46.92 3.95
5513 6289 0.824595 TCCAGACCTTCCGTCGAACA 60.825 55.000 0.00 0.00 46.92 3.18
5514 6290 0.666577 CCAGACCTTCCGTCGAACAC 60.667 60.000 0.00 0.00 46.92 3.32
5515 6291 1.002250 CAGACCTTCCGTCGAACACG 61.002 60.000 0.00 0.00 46.92 4.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
87 88 8.862325 TGATCAACCTGAACAACTTATATGTT 57.138 30.769 0.00 0.00 43.37 2.71
88 89 8.862325 TTGATCAACCTGAACAACTTATATGT 57.138 30.769 3.38 0.00 34.83 2.29
89 90 7.912250 GCTTGATCAACCTGAACAACTTATATG 59.088 37.037 3.38 0.00 34.83 1.78
90 91 7.201644 CGCTTGATCAACCTGAACAACTTATAT 60.202 37.037 3.38 0.00 34.83 0.86
93 94 4.213270 CGCTTGATCAACCTGAACAACTTA 59.787 41.667 3.38 0.00 34.83 2.24
95 96 2.549754 CGCTTGATCAACCTGAACAACT 59.450 45.455 3.38 0.00 34.83 3.16
99 113 4.742438 TTTACGCTTGATCAACCTGAAC 57.258 40.909 3.38 0.00 0.00 3.18
104 118 7.640240 GTCAATCTATTTTACGCTTGATCAACC 59.360 37.037 3.38 0.00 0.00 3.77
127 141 5.813672 GGCCATTTAGTTAATCACTACGTCA 59.186 40.000 0.00 0.00 37.74 4.35
178 192 9.346725 GGAAGAACATGTTAATTAAGCTTTCAG 57.653 33.333 11.95 0.00 0.00 3.02
216 280 1.904990 GAGCTTGTCAGGGGAGGACC 61.905 65.000 0.00 0.00 34.36 4.46
264 341 6.345096 TGTAGTCAGAATGTCAGAATGTCA 57.655 37.500 0.00 0.00 38.75 3.58
265 342 7.222417 CAGATGTAGTCAGAATGTCAGAATGTC 59.778 40.741 0.00 0.00 37.40 3.06
266 343 7.040494 CAGATGTAGTCAGAATGTCAGAATGT 58.960 38.462 0.00 0.00 37.40 2.71
267 344 7.263496 TCAGATGTAGTCAGAATGTCAGAATG 58.737 38.462 0.00 0.00 37.40 2.67
268 345 7.415592 TCAGATGTAGTCAGAATGTCAGAAT 57.584 36.000 0.00 0.00 37.40 2.40
269 346 6.840780 TCAGATGTAGTCAGAATGTCAGAA 57.159 37.500 0.00 0.00 37.40 3.02
270 347 6.604795 TCATCAGATGTAGTCAGAATGTCAGA 59.395 38.462 10.34 0.00 37.40 3.27
271 348 6.803642 TCATCAGATGTAGTCAGAATGTCAG 58.196 40.000 10.34 0.00 37.40 3.51
272 349 6.780457 TCATCAGATGTAGTCAGAATGTCA 57.220 37.500 10.34 0.00 37.40 3.58
304 381 2.905075 TCCTATCACACAAGGCATTCG 58.095 47.619 0.00 0.00 32.55 3.34
312 389 7.429374 AAGAGATCTTGATCCTATCACACAA 57.571 36.000 0.00 0.00 39.39 3.33
313 390 7.429374 AAAGAGATCTTGATCCTATCACACA 57.571 36.000 0.00 0.00 39.39 3.72
372 449 5.577100 ACAGAGGGTGTAGATGTTAGTACA 58.423 41.667 0.00 0.00 37.75 2.90
728 809 4.404324 GCTTCTTTACCTTTCGCTAAAGC 58.596 43.478 5.22 0.00 40.73 3.51
730 811 4.060205 ACGCTTCTTTACCTTTCGCTAAA 58.940 39.130 0.00 0.00 0.00 1.85
753 842 5.073144 ACACAAAAGGATAACCAGGAAGAGA 59.927 40.000 0.00 0.00 38.94 3.10
761 850 7.888021 AGAACATATCACACAAAAGGATAACCA 59.112 33.333 0.00 0.00 38.94 3.67
777 866 3.776969 AGGCCAGACAGAAGAACATATCA 59.223 43.478 5.01 0.00 0.00 2.15
780 869 4.640771 AAAGGCCAGACAGAAGAACATA 57.359 40.909 5.01 0.00 0.00 2.29
792 881 0.667993 CGACAAAGCAAAAGGCCAGA 59.332 50.000 5.01 0.00 46.50 3.86
882 971 0.878523 CGCTTCCACGACCAAGAACA 60.879 55.000 0.00 0.00 34.06 3.18
900 989 4.134187 ATGCTTTCGTGCGCGTCG 62.134 61.111 20.50 16.54 39.49 5.12
937 1028 0.322456 TGCTGCAACCTGGGACATAC 60.322 55.000 0.00 0.00 38.20 2.39
961 1053 3.001939 CCGTACGGTGCATAAAAGAATCC 59.998 47.826 26.39 0.00 0.00 3.01
1025 1117 1.032014 CTGGGAATAAACCATGGGCG 58.968 55.000 18.09 0.00 37.38 6.13
1060 1152 4.664150 AACACACCCACATAACCAAAAG 57.336 40.909 0.00 0.00 0.00 2.27
1063 1155 3.366396 ACAAACACACCCACATAACCAA 58.634 40.909 0.00 0.00 0.00 3.67
1117 1225 7.578310 AATTGGAAGGTTCATCATCATACAG 57.422 36.000 0.00 0.00 0.00 2.74
1138 1246 4.339247 GCACATTGTATGTCCAGCCTAATT 59.661 41.667 0.00 0.00 42.70 1.40
1143 1251 0.740737 GGCACATTGTATGTCCAGCC 59.259 55.000 4.52 4.52 42.70 4.85
1177 1285 2.353605 CCAACATGCAAACCCACATACC 60.354 50.000 0.00 0.00 0.00 2.73
1186 1294 2.417239 CCAATGATGCCAACATGCAAAC 59.583 45.455 0.00 0.00 45.84 2.93
1241 1425 1.395608 CACAACAAAGACCGAACGTGT 59.604 47.619 0.00 0.00 0.00 4.49
1258 1445 2.355363 GTACTGCACGACGCCACA 60.355 61.111 0.00 0.00 41.33 4.17
1297 1501 5.648526 GTCCATATCTAATAGGCTCGTCTCA 59.351 44.000 0.00 0.00 0.00 3.27
1299 1503 5.822204 AGTCCATATCTAATAGGCTCGTCT 58.178 41.667 0.00 0.00 0.00 4.18
1300 1504 7.627298 TTAGTCCATATCTAATAGGCTCGTC 57.373 40.000 0.00 0.00 0.00 4.20
1313 1517 4.706842 TGCCCCTCTTTTAGTCCATATC 57.293 45.455 0.00 0.00 0.00 1.63
1399 1603 6.271488 TGAGAATGCCCTATTTCAAAACAG 57.729 37.500 0.00 0.00 0.00 3.16
1419 1697 8.492673 TGTTAGTTATAACATCCTGCTTTGAG 57.507 34.615 17.65 0.00 44.94 3.02
1466 1744 2.225650 ACTACTCCCTCTGTCCCACAAT 60.226 50.000 0.00 0.00 0.00 2.71
1472 1750 3.088789 TGAGAACTACTCCCTCTGTCC 57.911 52.381 0.00 0.00 44.34 4.02
1476 1754 9.495382 ACTTATATTTTGAGAACTACTCCCTCT 57.505 33.333 0.00 0.00 44.34 3.69
1506 1784 5.046735 GCTAGGAAGAGCATCCATCTTATGA 60.047 44.000 6.07 0.00 42.27 2.15
1510 1788 2.371510 GGCTAGGAAGAGCATCCATCTT 59.628 50.000 6.07 0.00 44.76 2.40
1595 1878 2.470990 TCTGCTTGAGCTGGATTCCTA 58.529 47.619 3.95 0.00 42.66 2.94
1650 1957 0.591659 CAAGGCATGGATCGATGCTG 59.408 55.000 32.85 23.68 46.74 4.41
1676 1983 2.040412 GGGACAGAATTTCAGTCAGGGT 59.960 50.000 19.62 0.00 34.99 4.34
1725 2034 4.839668 TGTTTGTGGTATTTGTACTGCC 57.160 40.909 0.00 0.00 0.00 4.85
1732 2041 6.676950 TGTGCTCTTATGTTTGTGGTATTTG 58.323 36.000 0.00 0.00 0.00 2.32
1749 2058 2.363038 ACATGTGTTTGCATTGTGCTCT 59.637 40.909 0.00 0.00 45.31 4.09
1750 2059 2.473609 CACATGTGTTTGCATTGTGCTC 59.526 45.455 18.03 0.00 45.31 4.26
1869 2229 1.289276 TGTTGATGATGATGTCGCGG 58.711 50.000 6.13 0.00 0.00 6.46
1956 2317 2.758327 ATGAGCCGCTCCGTGGTA 60.758 61.111 17.81 0.00 35.34 3.25
1962 2323 2.512515 GTGACCATGAGCCGCTCC 60.513 66.667 17.81 2.40 0.00 4.70
2082 2443 1.153349 GAAGGAGGCGCGGAAGAAT 60.153 57.895 8.83 0.00 0.00 2.40
2109 2470 2.940514 TGTAGGACATGAAGGGGAGA 57.059 50.000 0.00 0.00 0.00 3.71
2412 2782 3.842925 AATGAGTTGCGCACGGGGT 62.843 57.895 11.12 0.00 0.00 4.95
2770 3140 0.249280 ACTGCGTGTTCGTCATCACA 60.249 50.000 0.00 0.00 39.49 3.58
2939 3345 1.542547 GGACCAGCTCGGACTTTTTGA 60.543 52.381 8.91 0.00 38.63 2.69
3018 3424 3.135712 TGTTCTCCAACTTGTGCTTCCTA 59.864 43.478 0.00 0.00 33.17 2.94
3072 3478 0.888619 AGTGCTCCATCTTTCGTCGA 59.111 50.000 0.00 0.00 0.00 4.20
3108 3514 2.813908 CGCGCTTGTAGGGTGTCC 60.814 66.667 5.56 0.00 34.46 4.02
3116 3522 2.650917 CGAGATCGCGCGCTTGTA 60.651 61.111 30.48 8.01 0.00 2.41
3228 3634 0.330604 TGGCCTGGTAGTACTCGTCT 59.669 55.000 3.32 0.00 0.00 4.18
3438 3844 1.843851 AGGAAGTTCACTTGGTGGACA 59.156 47.619 11.09 0.00 43.94 4.02
3651 4057 3.272334 CGGTGCTTCGCCCATAGC 61.272 66.667 0.00 0.00 37.89 2.97
3713 4119 2.728817 GCGGGTCGAGATAGTGGG 59.271 66.667 0.00 0.00 0.00 4.61
3924 4330 1.153086 GCTCATCTTGGGGTCGCAT 60.153 57.895 0.00 0.00 0.00 4.73
4228 4637 0.321564 TTCACCATGGCCGACTTCTG 60.322 55.000 13.04 0.00 0.00 3.02
4488 4921 1.141881 CGATGGAACCTGGTCCTCG 59.858 63.158 0.00 10.26 38.62 4.63
4520 4953 2.560981 TCGTGAGCCTGTGATCAAACTA 59.439 45.455 0.00 0.00 38.90 2.24
4579 5012 9.921637 ACTCTTCTCAAAACAACAACAAATAAA 57.078 25.926 0.00 0.00 0.00 1.40
4586 5019 4.029043 GCGACTCTTCTCAAAACAACAAC 58.971 43.478 0.00 0.00 0.00 3.32
4599 5032 8.818057 ACAACAAGTATTATTATGCGACTCTTC 58.182 33.333 0.00 0.00 0.00 2.87
4683 5118 5.350640 GGCTCATTACAGTATTATTACGCCC 59.649 44.000 0.00 0.00 33.32 6.13
4742 5179 1.421480 AGCTATGCCATCTCAGCTCA 58.579 50.000 0.00 0.00 40.25 4.26
4746 5183 3.611293 CGAGTGTAGCTATGCCATCTCAG 60.611 52.174 0.00 0.00 0.00 3.35
4841 5278 9.635520 AGCTCTGTGATTTTTCATCAAATTAAG 57.364 29.630 0.00 0.00 0.00 1.85
4845 5282 8.345724 AGTAGCTCTGTGATTTTTCATCAAAT 57.654 30.769 0.00 0.00 0.00 2.32
4846 5283 7.663081 AGAGTAGCTCTGTGATTTTTCATCAAA 59.337 33.333 0.00 0.00 39.62 2.69
4848 5285 6.705302 AGAGTAGCTCTGTGATTTTTCATCA 58.295 36.000 0.00 0.00 39.62 3.07
4878 5315 3.127376 TGTTCCGAGATGCATTGTGATTG 59.873 43.478 0.00 0.00 0.00 2.67
4995 5528 6.560003 TCCTCCTGCTACATCAAGATTAAA 57.440 37.500 0.00 0.00 0.00 1.52
5018 5703 9.613428 CATCCATTAATTACATATGACGGGTAT 57.387 33.333 10.38 0.00 0.00 2.73
5036 5721 8.620416 CGTGATTTGAAAATAGTCCATCCATTA 58.380 33.333 0.00 0.00 0.00 1.90
5037 5722 7.416664 CCGTGATTTGAAAATAGTCCATCCATT 60.417 37.037 0.00 0.00 0.00 3.16
5038 5723 6.039717 CCGTGATTTGAAAATAGTCCATCCAT 59.960 38.462 0.00 0.00 0.00 3.41
5039 5724 5.356751 CCGTGATTTGAAAATAGTCCATCCA 59.643 40.000 0.00 0.00 0.00 3.41
5207 5954 2.916269 TGTGGAGGTATTCATTGTCCCA 59.084 45.455 0.00 0.00 0.00 4.37
5209 5956 4.636206 GTCTTGTGGAGGTATTCATTGTCC 59.364 45.833 0.00 0.00 0.00 4.02
5292 6054 3.053831 TGTTGCCCTAAAGTCTAGCAC 57.946 47.619 0.00 0.00 32.18 4.40
5477 6253 0.179097 GGACGCCAAGAGCTAAGAGG 60.179 60.000 0.00 0.00 40.39 3.69
5478 6254 0.532573 TGGACGCCAAGAGCTAAGAG 59.467 55.000 0.00 0.00 40.39 2.85
5479 6255 0.532573 CTGGACGCCAAGAGCTAAGA 59.467 55.000 0.00 0.00 40.39 2.10
5480 6256 0.532573 TCTGGACGCCAAGAGCTAAG 59.467 55.000 0.00 0.00 40.39 2.18
5481 6257 0.246635 GTCTGGACGCCAAGAGCTAA 59.753 55.000 0.00 0.00 40.39 3.09
5482 6258 1.605058 GGTCTGGACGCCAAGAGCTA 61.605 60.000 0.00 0.00 40.39 3.32
5483 6259 2.659610 GTCTGGACGCCAAGAGCT 59.340 61.111 0.00 0.00 40.39 4.09
5484 6260 2.435059 GGTCTGGACGCCAAGAGC 60.435 66.667 0.00 0.00 30.80 4.09
5485 6261 0.390472 GAAGGTCTGGACGCCAAGAG 60.390 60.000 0.35 0.00 30.80 2.85
5486 6262 1.671742 GAAGGTCTGGACGCCAAGA 59.328 57.895 0.35 0.00 30.80 3.02
5487 6263 1.376037 GGAAGGTCTGGACGCCAAG 60.376 63.158 0.35 0.00 30.80 3.61
5488 6264 2.747686 GGAAGGTCTGGACGCCAA 59.252 61.111 0.35 0.00 30.80 4.52
5489 6265 3.691342 CGGAAGGTCTGGACGCCA 61.691 66.667 0.00 0.00 0.00 5.69
5490 6266 3.644399 GACGGAAGGTCTGGACGCC 62.644 68.421 0.00 0.00 42.62 5.68
5491 6267 2.126031 GACGGAAGGTCTGGACGC 60.126 66.667 0.00 0.00 42.62 5.19
5492 6268 1.859427 TTCGACGGAAGGTCTGGACG 61.859 60.000 0.00 0.00 43.79 4.79
5493 6269 0.388263 GTTCGACGGAAGGTCTGGAC 60.388 60.000 0.00 0.00 43.79 4.02
5494 6270 0.824595 TGTTCGACGGAAGGTCTGGA 60.825 55.000 0.00 0.00 43.79 3.86
5495 6271 0.666577 GTGTTCGACGGAAGGTCTGG 60.667 60.000 0.00 0.00 43.79 3.86
5496 6272 1.002250 CGTGTTCGACGGAAGGTCTG 61.002 60.000 0.00 0.00 44.85 3.51
5497 6273 1.285023 CGTGTTCGACGGAAGGTCT 59.715 57.895 0.00 0.00 44.85 3.85
5498 6274 3.838468 CGTGTTCGACGGAAGGTC 58.162 61.111 0.00 0.00 44.85 3.85


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

AutoCloner maintained by Alex Coulton.