Multiple sequence alignment - TraesCS3A01G160700

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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 TraesCS3A01G160700 chr3A 100.000 4481 0 0 1 4481 161445296 161449776 0.000000e+00 8275
1 TraesCS3A01G160700 chr3A 94.792 96 4 1 4159 4253 686127449 686127544 1.000000e-31 148
2 TraesCS3A01G160700 chr3A 91.743 109 5 4 4160 4265 750297225 750297118 1.000000e-31 148
3 TraesCS3A01G160700 chr3D 94.281 4144 149 32 75 4164 142475569 142479678 0.000000e+00 6259
4 TraesCS3A01G160700 chr3D 95.885 243 7 3 4241 4481 142479673 142479914 1.510000e-104 390
5 TraesCS3A01G160700 chr3B 93.068 3722 161 43 1 3654 204280851 204284543 0.000000e+00 5354
6 TraesCS3A01G160700 chr3B 97.070 512 15 0 3651 4162 204284625 204285136 0.000000e+00 863
7 TraesCS3A01G160700 chr3B 92.308 247 11 5 4241 4481 204285133 204285377 1.190000e-90 344
8 TraesCS3A01G160700 chr7D 97.753 89 1 1 4158 4245 45835415 45835327 7.760000e-33 152
9 TraesCS3A01G160700 chr2A 97.727 88 2 0 4158 4245 694958722 694958635 7.760000e-33 152
10 TraesCS3A01G160700 chr1A 94.000 100 4 2 4154 4251 584082806 584082905 2.790000e-32 150
11 TraesCS3A01G160700 chr7A 94.792 96 2 3 4151 4244 3013999 3014093 3.610000e-31 147
12 TraesCS3A01G160700 chr7B 89.076 119 10 3 4151 4266 414314443 414314561 1.300000e-30 145
13 TraesCS3A01G160700 chr2D 96.552 87 2 1 4160 4245 404795833 404795919 4.670000e-30 143
14 TraesCS3A01G160700 chr2D 86.777 121 11 5 4158 4276 233382218 233382101 3.640000e-26 130


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 TraesCS3A01G160700 chr3A 161445296 161449776 4480 False 8275.0 8275 100.000000 1 4481 1 chr3A.!!$F1 4480
1 TraesCS3A01G160700 chr3D 142475569 142479914 4345 False 3324.5 6259 95.083000 75 4481 2 chr3D.!!$F1 4406
2 TraesCS3A01G160700 chr3B 204280851 204285377 4526 False 2187.0 5354 94.148667 1 4481 3 chr3B.!!$F1 4480

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
247 293 0.113190 GGGGATGGGGTCATGATTCC 59.887 60.0 0.00 4.46 32.98 3.01 F
1052 1115 0.537188 TCATCGGAGGAGGCAGAAAC 59.463 55.0 0.00 0.00 0.00 2.78 F
2367 2449 0.035317 TGGGCATATCGATGGTGCTC 59.965 55.0 26.36 24.80 39.76 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1634 1710 0.687354 AGTTCATCACCTTCCGCAGT 59.313 50.000 0.0 0.0 0.0 4.40 R
2976 3058 0.034767 CTCCCAGATGCTCTTTGCCA 60.035 55.000 0.0 0.0 42.0 4.92 R
4234 4403 1.214673 TGGCTATGACGTACTCCCTCT 59.785 52.381 0.0 0.0 0.0 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
46 47 8.761575 TTCTTTTTCCTTTAATGTCATGCATC 57.238 30.769 0.00 0.00 36.67 3.91
68 69 7.307870 GCATCACAGAGAAAAGCATCCTAATAG 60.308 40.741 0.00 0.00 0.00 1.73
69 70 6.051717 TCACAGAGAAAAGCATCCTAATAGC 58.948 40.000 0.00 0.00 0.00 2.97
70 71 6.054295 CACAGAGAAAAGCATCCTAATAGCT 58.946 40.000 0.00 0.00 41.03 3.32
72 73 6.765512 ACAGAGAAAAGCATCCTAATAGCTTC 59.234 38.462 0.00 0.00 46.95 3.86
73 74 6.765036 CAGAGAAAAGCATCCTAATAGCTTCA 59.235 38.462 0.00 0.00 46.95 3.02
83 108 7.228308 GCATCCTAATAGCTTCACTTCTTTCAT 59.772 37.037 0.00 0.00 0.00 2.57
121 149 2.228822 GCATGGTGAACTTACAACCCAG 59.771 50.000 0.00 0.00 0.00 4.45
127 155 2.706723 TGAACTTACAACCCAGTGGCTA 59.293 45.455 2.61 0.00 33.59 3.93
136 164 4.080015 ACAACCCAGTGGCTATTATAAGCA 60.080 41.667 2.61 0.00 44.64 3.91
144 172 4.932200 GTGGCTATTATAAGCAGCAGTAGG 59.068 45.833 18.52 0.00 44.64 3.18
174 202 6.461927 CCACCTTTTGATGTTATGCATGCTAT 60.462 38.462 20.33 12.94 38.06 2.97
175 203 6.639686 CACCTTTTGATGTTATGCATGCTATC 59.360 38.462 20.33 14.09 38.06 2.08
219 265 5.164620 TCTTAGTTGCTCATGGTCATTGA 57.835 39.130 0.00 0.00 0.00 2.57
221 267 5.645067 TCTTAGTTGCTCATGGTCATTGAAG 59.355 40.000 0.00 0.00 0.00 3.02
234 280 5.307976 TGGTCATTGAAGAGTATAGGGGATG 59.692 44.000 0.00 0.00 0.00 3.51
235 281 5.280215 GGTCATTGAAGAGTATAGGGGATGG 60.280 48.000 0.00 0.00 0.00 3.51
236 282 4.846367 TCATTGAAGAGTATAGGGGATGGG 59.154 45.833 0.00 0.00 0.00 4.00
237 283 3.275848 TGAAGAGTATAGGGGATGGGG 57.724 52.381 0.00 0.00 0.00 4.96
239 285 3.174779 GAAGAGTATAGGGGATGGGGTC 58.825 54.545 0.00 0.00 0.00 4.46
240 286 2.161624 AGAGTATAGGGGATGGGGTCA 58.838 52.381 0.00 0.00 0.00 4.02
241 287 2.735906 AGAGTATAGGGGATGGGGTCAT 59.264 50.000 0.00 0.00 36.09 3.06
242 288 2.840651 GAGTATAGGGGATGGGGTCATG 59.159 54.545 0.00 0.00 32.98 3.07
243 289 2.458706 AGTATAGGGGATGGGGTCATGA 59.541 50.000 0.00 0.00 32.98 3.07
244 290 2.769011 ATAGGGGATGGGGTCATGAT 57.231 50.000 0.00 0.00 32.98 2.45
245 291 2.531177 TAGGGGATGGGGTCATGATT 57.469 50.000 0.00 0.00 32.98 2.57
246 292 1.152649 AGGGGATGGGGTCATGATTC 58.847 55.000 0.00 0.00 32.98 2.52
247 293 0.113190 GGGGATGGGGTCATGATTCC 59.887 60.000 0.00 4.46 32.98 3.01
248 294 1.152649 GGGATGGGGTCATGATTCCT 58.847 55.000 15.38 4.67 32.98 3.36
249 295 2.348472 GGGATGGGGTCATGATTCCTA 58.652 52.381 15.38 11.24 32.98 2.94
250 296 2.040412 GGGATGGGGTCATGATTCCTAC 59.960 54.545 15.38 10.31 32.98 3.18
251 297 2.982488 GGATGGGGTCATGATTCCTACT 59.018 50.000 15.38 4.10 32.98 2.57
252 298 3.008485 GGATGGGGTCATGATTCCTACTC 59.992 52.174 15.38 10.47 32.98 2.59
253 299 3.421394 TGGGGTCATGATTCCTACTCT 57.579 47.619 15.38 0.00 0.00 3.24
254 300 4.552883 TGGGGTCATGATTCCTACTCTA 57.447 45.455 15.38 0.00 0.00 2.43
255 301 5.093236 TGGGGTCATGATTCCTACTCTAT 57.907 43.478 15.38 0.00 0.00 1.98
256 302 5.476983 TGGGGTCATGATTCCTACTCTATT 58.523 41.667 15.38 0.00 0.00 1.73
257 303 5.911178 TGGGGTCATGATTCCTACTCTATTT 59.089 40.000 15.38 0.00 0.00 1.40
258 304 6.043243 TGGGGTCATGATTCCTACTCTATTTC 59.957 42.308 15.38 0.25 0.00 2.17
259 305 6.043243 GGGGTCATGATTCCTACTCTATTTCA 59.957 42.308 14.95 0.00 0.00 2.69
260 306 7.256835 GGGGTCATGATTCCTACTCTATTTCAT 60.257 40.741 14.95 0.00 0.00 2.57
261 307 7.605691 GGGTCATGATTCCTACTCTATTTCATG 59.394 40.741 0.00 0.00 40.01 3.07
296 342 4.904251 ACTATGGACTGATGGTATGCTCTT 59.096 41.667 0.00 0.00 0.00 2.85
297 343 3.827008 TGGACTGATGGTATGCTCTTC 57.173 47.619 0.00 0.00 0.00 2.87
300 346 3.494048 GGACTGATGGTATGCTCTTCCTG 60.494 52.174 0.00 0.00 0.00 3.86
487 533 2.388232 CGAGCTGGTTAACGTGGCC 61.388 63.158 0.00 0.00 0.00 5.36
553 599 9.507280 AAAACGAAGCACTATGAATGAATATTG 57.493 29.630 0.00 0.00 0.00 1.90
561 607 7.073883 CACTATGAATGAATATTGTCAAGCCG 58.926 38.462 0.00 0.00 0.00 5.52
760 806 3.242252 GCGCTGAGCTTTAGAGATCAAAC 60.242 47.826 1.78 0.00 46.70 2.93
781 827 3.378112 ACGGAATGAACTGCCATTACATG 59.622 43.478 0.00 0.00 37.24 3.21
802 848 4.346970 TGTTGTGTTGAATTGCTGTTACG 58.653 39.130 0.00 0.00 0.00 3.18
821 867 9.820229 CTGTTACGTTGTGTTGATGTTATATTT 57.180 29.630 0.00 0.00 0.00 1.40
847 893 4.527564 GTGTCCAGAACAGAATTTTCGTG 58.472 43.478 0.00 0.00 38.97 4.35
865 911 2.414138 CGTGGAGATCCGGTAAAACAAC 59.586 50.000 0.00 0.00 39.43 3.32
1014 1074 3.254024 AAACATGGCTCCCGTCGCT 62.254 57.895 0.00 0.00 0.00 4.93
1052 1115 0.537188 TCATCGGAGGAGGCAGAAAC 59.463 55.000 0.00 0.00 0.00 2.78
1400 1463 2.424523 CCACCCTCTCCTTCTACGGTAT 60.425 54.545 0.00 0.00 0.00 2.73
1470 1546 4.474846 CCGGCGGCCGTGATTTTG 62.475 66.667 36.22 17.86 46.80 2.44
1617 1693 4.373116 TCGTCACCTTCGCCAGCC 62.373 66.667 0.00 0.00 0.00 4.85
1634 1710 2.528818 CCTGTTCTGCACCCTCCCA 61.529 63.158 0.00 0.00 0.00 4.37
1648 1724 1.903877 CTCCCACTGCGGAAGGTGAT 61.904 60.000 0.00 0.00 36.56 3.06
1650 1726 1.296392 CCACTGCGGAAGGTGATGA 59.704 57.895 0.00 0.00 36.56 2.92
1651 1727 0.321564 CCACTGCGGAAGGTGATGAA 60.322 55.000 0.00 0.00 36.56 2.57
1652 1728 0.798776 CACTGCGGAAGGTGATGAAC 59.201 55.000 0.00 0.00 35.69 3.18
1654 1730 1.338200 ACTGCGGAAGGTGATGAACTC 60.338 52.381 0.00 0.00 0.00 3.01
1655 1731 0.684535 TGCGGAAGGTGATGAACTCA 59.315 50.000 0.00 0.00 0.00 3.41
1656 1732 1.278985 TGCGGAAGGTGATGAACTCAT 59.721 47.619 0.00 0.00 39.70 2.90
1657 1733 2.290260 TGCGGAAGGTGATGAACTCATT 60.290 45.455 0.00 0.00 36.57 2.57
1658 1734 2.749621 GCGGAAGGTGATGAACTCATTT 59.250 45.455 0.00 0.00 36.57 2.32
1659 1735 3.181506 GCGGAAGGTGATGAACTCATTTC 60.182 47.826 0.00 0.00 36.57 2.17
1661 1737 3.375299 GGAAGGTGATGAACTCATTTCCG 59.625 47.826 5.53 0.00 39.05 4.30
1663 1739 4.494091 AGGTGATGAACTCATTTCCGAT 57.506 40.909 0.00 0.00 36.57 4.18
1664 1740 4.446371 AGGTGATGAACTCATTTCCGATC 58.554 43.478 0.00 0.00 36.57 3.69
1666 1742 4.034510 GGTGATGAACTCATTTCCGATCAC 59.965 45.833 0.00 0.00 42.09 3.06
1668 1744 6.042777 GTGATGAACTCATTTCCGATCACTA 58.957 40.000 0.00 0.00 40.87 2.74
1669 1745 6.703607 GTGATGAACTCATTTCCGATCACTAT 59.296 38.462 0.00 0.00 40.87 2.12
1670 1746 7.225538 GTGATGAACTCATTTCCGATCACTATT 59.774 37.037 0.00 0.00 40.87 1.73
1671 1747 7.770433 TGATGAACTCATTTCCGATCACTATTT 59.230 33.333 0.00 0.00 36.57 1.40
1672 1748 7.921786 TGAACTCATTTCCGATCACTATTTT 57.078 32.000 0.00 0.00 32.58 1.82
1673 1749 7.751732 TGAACTCATTTCCGATCACTATTTTG 58.248 34.615 0.00 0.00 32.58 2.44
1674 1750 7.606073 TGAACTCATTTCCGATCACTATTTTGA 59.394 33.333 0.00 0.00 32.58 2.69
1681 1760 4.756642 TCCGATCACTATTTTGATCCATGC 59.243 41.667 7.38 0.00 46.37 4.06
1691 1770 6.982160 ATTTTGATCCATGCCTTTGCTATA 57.018 33.333 0.00 0.00 38.71 1.31
1692 1771 6.788598 TTTTGATCCATGCCTTTGCTATAA 57.211 33.333 0.00 0.00 38.71 0.98
1800 1879 0.874175 TCGTCAACAGCTTCCACACG 60.874 55.000 0.00 0.00 0.00 4.49
1827 1906 0.166814 GAGCCGCAACAGCAAAGTAG 59.833 55.000 0.00 0.00 0.00 2.57
1829 1908 0.804989 GCCGCAACAGCAAAGTAGAT 59.195 50.000 0.00 0.00 0.00 1.98
1855 1934 1.672737 GCCATTTTGTAACCTGCTGGC 60.673 52.381 9.95 0.00 40.68 4.85
1889 1968 2.663606 CGTTTGTAAGCTTAACCGGCAC 60.664 50.000 7.99 0.00 0.00 5.01
1892 1971 3.681593 TGTAAGCTTAACCGGCACTAA 57.318 42.857 7.99 0.00 0.00 2.24
1927 2006 1.524482 CTCCTTAGGAGGCAGGTGC 59.476 63.158 20.07 0.00 45.43 5.01
1995 2074 1.002990 GTGGGTTTACACGGGAGGG 60.003 63.158 0.00 0.00 40.95 4.30
2043 2122 3.065371 CCTTGTTCGGATTGAAGGCATAC 59.935 47.826 0.00 0.00 37.23 2.39
2152 2231 5.893500 TCGGATCTATCATTACCTCCTTCT 58.106 41.667 0.00 0.00 0.00 2.85
2256 2338 5.304686 ACAAGGTTAGTGACAGAATTCCA 57.695 39.130 0.65 0.00 0.00 3.53
2270 2352 4.256920 AGAATTCCATCTGAACTTCACCG 58.743 43.478 0.65 0.00 35.31 4.94
2367 2449 0.035317 TGGGCATATCGATGGTGCTC 59.965 55.000 26.36 24.80 39.76 4.26
2376 2458 2.124151 ATGGTGCTCGGGGATTGC 60.124 61.111 0.00 0.00 0.00 3.56
2426 2508 1.181098 GCTGCCAACCACTTCCACAT 61.181 55.000 0.00 0.00 0.00 3.21
2538 2620 4.394300 CGCAGGAACAAGATCTTTCTGAAT 59.606 41.667 20.17 3.55 30.72 2.57
2628 2710 2.430694 TCCACGTATCTTCCCACAGATG 59.569 50.000 0.00 0.00 35.08 2.90
2671 2753 1.109920 ATACGCTGTCGCTCCCATCT 61.110 55.000 0.00 0.00 39.84 2.90
2722 2804 1.847506 TGTGACTGGTCCCTGGCAT 60.848 57.895 1.78 0.00 35.42 4.40
2730 2812 1.122019 GGTCCCTGGCATCCGTCTAT 61.122 60.000 0.00 0.00 0.00 1.98
2838 2920 3.449377 TGTTGATGATCATTGGCAATGCT 59.551 39.130 30.62 23.70 38.77 3.79
2889 2971 1.153823 CCTAACACTCACCTCGCCG 60.154 63.158 0.00 0.00 0.00 6.46
2895 2977 4.056125 CTCACCTCGCCGCTGTCA 62.056 66.667 0.00 0.00 0.00 3.58
2912 2994 4.082571 GCTGTCAATGTTCATAAGCCAAGT 60.083 41.667 0.00 0.00 0.00 3.16
2976 3058 4.266714 TCCTGTCCTTCGAAAAACTTGTT 58.733 39.130 0.00 0.00 0.00 2.83
3161 3243 1.198637 GTCAGCAGTAGCCAAAGCAAG 59.801 52.381 0.00 0.00 43.56 4.01
3336 3418 7.041721 CAGTTGTAGTAGCATCAGGTTTGATA 58.958 38.462 0.00 0.00 42.12 2.15
3431 3513 7.290110 TGAAGTTCTTGTCTAGTCATCAGAA 57.710 36.000 4.17 1.46 0.00 3.02
3436 3518 6.901081 TCTTGTCTAGTCATCAGAACAAGA 57.099 37.500 12.75 12.75 37.57 3.02
3605 3688 3.387699 ACTTGCCTTTTTGCCTGTGTAAT 59.612 39.130 0.00 0.00 0.00 1.89
3607 3690 4.414337 TGCCTTTTTGCCTGTGTAATTT 57.586 36.364 0.00 0.00 0.00 1.82
3896 4065 4.884164 GGTTAATGAAGATGAAGGTGGGAG 59.116 45.833 0.00 0.00 0.00 4.30
4044 4213 0.181114 TGGCAGGTCAGCATCATACC 59.819 55.000 0.00 0.00 35.83 2.73
4164 4333 5.416271 TTCCAGGGTGTTTCATAGTACTC 57.584 43.478 0.00 0.00 0.00 2.59
4165 4334 3.773119 TCCAGGGTGTTTCATAGTACTCC 59.227 47.826 0.00 0.00 0.00 3.85
4166 4335 3.118371 CCAGGGTGTTTCATAGTACTCCC 60.118 52.174 0.00 0.59 44.62 4.30
4168 4337 4.403585 GGGTGTTTCATAGTACTCCCTC 57.596 50.000 0.00 0.00 42.25 4.30
4169 4338 3.134262 GGGTGTTTCATAGTACTCCCTCC 59.866 52.174 0.00 0.00 42.25 4.30
4170 4339 3.181478 GGTGTTTCATAGTACTCCCTCCG 60.181 52.174 0.00 0.00 0.00 4.63
4171 4340 3.446516 GTGTTTCATAGTACTCCCTCCGT 59.553 47.826 0.00 0.00 0.00 4.69
4172 4341 4.641989 GTGTTTCATAGTACTCCCTCCGTA 59.358 45.833 0.00 0.00 0.00 4.02
4173 4342 5.126061 GTGTTTCATAGTACTCCCTCCGTAA 59.874 44.000 0.00 0.00 0.00 3.18
4174 4343 5.716228 TGTTTCATAGTACTCCCTCCGTAAA 59.284 40.000 0.00 0.00 0.00 2.01
4175 4344 5.841957 TTCATAGTACTCCCTCCGTAAAC 57.158 43.478 0.00 0.00 0.00 2.01
4176 4345 5.121380 TCATAGTACTCCCTCCGTAAACT 57.879 43.478 0.00 0.00 0.00 2.66
4177 4346 6.252599 TCATAGTACTCCCTCCGTAAACTA 57.747 41.667 0.00 0.00 0.00 2.24
4178 4347 6.662755 TCATAGTACTCCCTCCGTAAACTAA 58.337 40.000 0.00 0.00 0.00 2.24
4179 4348 7.293073 TCATAGTACTCCCTCCGTAAACTAAT 58.707 38.462 0.00 0.00 0.00 1.73
4180 4349 8.439971 TCATAGTACTCCCTCCGTAAACTAATA 58.560 37.037 0.00 0.00 0.00 0.98
4181 4350 9.240734 CATAGTACTCCCTCCGTAAACTAATAT 57.759 37.037 0.00 0.00 0.00 1.28
4184 4353 9.294614 AGTACTCCCTCCGTAAACTAATATAAG 57.705 37.037 0.00 0.00 0.00 1.73
4185 4354 9.289782 GTACTCCCTCCGTAAACTAATATAAGA 57.710 37.037 0.00 0.00 0.00 2.10
4186 4355 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
4187 4356 8.003629 ACTCCCTCCGTAAACTAATATAAGAGT 58.996 37.037 0.00 0.00 0.00 3.24
4188 4357 8.174733 TCCCTCCGTAAACTAATATAAGAGTG 57.825 38.462 0.00 0.00 0.00 3.51
4189 4358 7.781693 TCCCTCCGTAAACTAATATAAGAGTGT 59.218 37.037 0.00 0.00 0.00 3.55
4190 4359 8.419442 CCCTCCGTAAACTAATATAAGAGTGTT 58.581 37.037 0.00 0.00 0.00 3.32
4191 4360 9.813446 CCTCCGTAAACTAATATAAGAGTGTTT 57.187 33.333 0.00 0.00 0.00 2.83
4239 4408 8.522542 ACACTCTTATAGTAGTTTACAGAGGG 57.477 38.462 0.00 0.00 35.76 4.30
4240 4409 8.334734 ACACTCTTATAGTAGTTTACAGAGGGA 58.665 37.037 2.59 0.00 35.76 4.20
4241 4410 8.842280 CACTCTTATAGTAGTTTACAGAGGGAG 58.158 40.741 0.00 0.00 35.76 4.30
4242 4411 8.559175 ACTCTTATAGTAGTTTACAGAGGGAGT 58.441 37.037 0.00 0.00 36.36 3.85
4244 4413 9.844257 TCTTATAGTAGTTTACAGAGGGAGTAC 57.156 37.037 0.00 0.00 0.00 2.73
4245 4414 8.668510 TTATAGTAGTTTACAGAGGGAGTACG 57.331 38.462 0.00 0.00 0.00 3.67
4260 4429 4.189231 GGAGTACGTCATAGCCAAATGTT 58.811 43.478 0.00 0.00 0.00 2.71
4291 4463 5.817988 TCAGTTTCTCTACGATATGAACGG 58.182 41.667 0.00 0.00 34.93 4.44
4470 4644 8.879759 TGTCCGCTTAGAACTTTTAGATATTTG 58.120 33.333 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 5.945191 TCTGTGATGCATGACATTAAAGGAA 59.055 36.000 19.53 0.00 39.84 3.36
34 35 5.621555 GCTTTTCTCTGTGATGCATGACATT 60.622 40.000 19.53 0.00 39.84 2.71
42 43 3.015327 AGGATGCTTTTCTCTGTGATGC 58.985 45.455 0.00 0.00 0.00 3.91
46 47 6.054295 AGCTATTAGGATGCTTTTCTCTGTG 58.946 40.000 0.00 0.00 32.61 3.66
94 119 6.451393 GGTTGTAAGTTCACCATGCAATTTA 58.549 36.000 0.00 0.00 0.00 1.40
95 120 5.296748 GGTTGTAAGTTCACCATGCAATTT 58.703 37.500 0.00 0.00 0.00 1.82
96 121 4.262420 GGGTTGTAAGTTCACCATGCAATT 60.262 41.667 0.00 0.00 0.00 2.32
112 140 5.131308 TGCTTATAATAGCCACTGGGTTGTA 59.869 40.000 4.78 0.00 40.49 2.41
121 149 4.932200 CCTACTGCTGCTTATAATAGCCAC 59.068 45.833 15.34 0.91 40.49 5.01
127 155 5.839063 TGGTAGTCCTACTGCTGCTTATAAT 59.161 40.000 0.00 0.00 36.36 1.28
136 164 2.625282 AAGGTGGTAGTCCTACTGCT 57.375 50.000 4.58 0.00 36.36 4.24
144 172 5.414454 TGCATAACATCAAAAGGTGGTAGTC 59.586 40.000 0.00 0.00 0.00 2.59
198 244 5.645067 TCTTCAATGACCATGAGCAACTAAG 59.355 40.000 0.00 0.00 0.00 2.18
219 265 2.527057 TGACCCCATCCCCTATACTCTT 59.473 50.000 0.00 0.00 0.00 2.85
221 267 2.715763 TGACCCCATCCCCTATACTC 57.284 55.000 0.00 0.00 0.00 2.59
234 280 6.043243 TGAAATAGAGTAGGAATCATGACCCC 59.957 42.308 11.28 9.21 0.00 4.95
235 281 7.067496 TGAAATAGAGTAGGAATCATGACCC 57.933 40.000 0.00 2.27 0.00 4.46
236 282 8.370940 TCATGAAATAGAGTAGGAATCATGACC 58.629 37.037 10.52 0.00 43.82 4.02
239 285 9.939802 TCATCATGAAATAGAGTAGGAATCATG 57.060 33.333 0.00 6.53 42.35 3.07
241 287 9.939802 CATCATCATGAAATAGAGTAGGAATCA 57.060 33.333 0.00 0.00 30.57 2.57
242 288 8.881743 GCATCATCATGAAATAGAGTAGGAATC 58.118 37.037 0.00 0.00 30.57 2.52
243 289 8.380867 TGCATCATCATGAAATAGAGTAGGAAT 58.619 33.333 0.00 0.00 30.57 3.01
244 290 7.738847 TGCATCATCATGAAATAGAGTAGGAA 58.261 34.615 0.00 0.00 30.57 3.36
245 291 7.307131 TGCATCATCATGAAATAGAGTAGGA 57.693 36.000 0.00 0.00 30.57 2.94
246 292 7.606839 ACATGCATCATCATGAAATAGAGTAGG 59.393 37.037 0.00 0.00 44.94 3.18
247 293 8.549338 ACATGCATCATCATGAAATAGAGTAG 57.451 34.615 0.00 0.00 44.94 2.57
248 294 9.428097 GTACATGCATCATCATGAAATAGAGTA 57.572 33.333 0.00 0.00 44.94 2.59
249 295 8.155510 AGTACATGCATCATCATGAAATAGAGT 58.844 33.333 0.00 0.00 44.94 3.24
250 296 8.549338 AGTACATGCATCATCATGAAATAGAG 57.451 34.615 0.00 0.00 44.94 2.43
253 299 9.169592 CCATAGTACATGCATCATCATGAAATA 57.830 33.333 0.00 0.00 44.94 1.40
254 300 7.886446 TCCATAGTACATGCATCATCATGAAAT 59.114 33.333 0.00 0.00 44.94 2.17
255 301 7.173735 GTCCATAGTACATGCATCATCATGAAA 59.826 37.037 0.00 0.00 44.94 2.69
256 302 6.652062 GTCCATAGTACATGCATCATCATGAA 59.348 38.462 0.00 0.00 44.94 2.57
257 303 6.013984 AGTCCATAGTACATGCATCATCATGA 60.014 38.462 10.31 0.00 44.94 3.07
258 304 6.092259 CAGTCCATAGTACATGCATCATCATG 59.908 42.308 0.00 2.54 46.86 3.07
259 305 6.013984 TCAGTCCATAGTACATGCATCATCAT 60.014 38.462 0.00 0.00 0.00 2.45
260 306 5.305128 TCAGTCCATAGTACATGCATCATCA 59.695 40.000 0.00 0.00 0.00 3.07
261 307 5.787380 TCAGTCCATAGTACATGCATCATC 58.213 41.667 0.00 0.00 0.00 2.92
487 533 5.689819 CAGGGAAACTTCAACAATTACTCG 58.310 41.667 0.00 0.00 0.00 4.18
553 599 1.235724 AAGCTTACCAACGGCTTGAC 58.764 50.000 0.00 0.00 43.44 3.18
561 607 9.353999 CCATAAGAAATAAACAAGCTTACCAAC 57.646 33.333 0.00 0.00 0.00 3.77
760 806 3.956233 CATGTAATGGCAGTTCATTCCG 58.044 45.455 4.26 0.00 41.79 4.30
781 827 4.347813 ACGTAACAGCAATTCAACACAAC 58.652 39.130 0.00 0.00 0.00 3.32
802 848 6.033407 CACGGCAAATATAACATCAACACAAC 59.967 38.462 0.00 0.00 0.00 3.32
821 867 0.396435 ATTCTGTTCTGGACACGGCA 59.604 50.000 0.00 0.00 33.82 5.69
847 893 3.671716 ACTGTTGTTTTACCGGATCTCC 58.328 45.455 9.46 0.00 0.00 3.71
1014 1074 4.386951 CGTGGATGCCGGTGACCA 62.387 66.667 1.90 7.45 0.00 4.02
1033 1093 0.537188 GTTTCTGCCTCCTCCGATGA 59.463 55.000 0.00 0.00 0.00 2.92
1034 1094 0.539051 AGTTTCTGCCTCCTCCGATG 59.461 55.000 0.00 0.00 0.00 3.84
1035 1095 0.539051 CAGTTTCTGCCTCCTCCGAT 59.461 55.000 0.00 0.00 0.00 4.18
1086 1149 1.694133 CCTCCACTGATGGCTCCTCC 61.694 65.000 0.00 0.00 46.80 4.30
1098 1161 4.681978 GCGAACGCCACCTCCACT 62.682 66.667 8.03 0.00 34.56 4.00
1470 1546 1.501169 GTGAAACCACCTGCAAATGC 58.499 50.000 0.00 0.00 42.50 3.56
1617 1693 1.302832 GTGGGAGGGTGCAGAACAG 60.303 63.158 0.00 0.00 0.00 3.16
1634 1710 0.687354 AGTTCATCACCTTCCGCAGT 59.313 50.000 0.00 0.00 0.00 4.40
1648 1724 7.606073 TCAAAATAGTGATCGGAAATGAGTTCA 59.394 33.333 0.00 0.00 38.06 3.18
1650 1726 7.921786 TCAAAATAGTGATCGGAAATGAGTT 57.078 32.000 0.00 0.00 0.00 3.01
1651 1727 8.147642 GATCAAAATAGTGATCGGAAATGAGT 57.852 34.615 0.00 0.00 43.27 3.41
1661 1737 8.421870 GCAAAGGCATGGATCAAAATAGTGATC 61.422 40.741 6.63 6.63 44.88 2.92
1663 1739 5.394443 GCAAAGGCATGGATCAAAATAGTGA 60.394 40.000 0.00 0.00 40.72 3.41
1664 1740 4.807304 GCAAAGGCATGGATCAAAATAGTG 59.193 41.667 0.00 0.00 40.72 2.74
1666 1742 5.272283 AGCAAAGGCATGGATCAAAATAG 57.728 39.130 0.00 0.00 44.61 1.73
1668 1744 5.881923 ATAGCAAAGGCATGGATCAAAAT 57.118 34.783 0.00 0.00 44.61 1.82
1669 1745 6.788598 TTATAGCAAAGGCATGGATCAAAA 57.211 33.333 0.00 0.00 44.61 2.44
1670 1746 6.788598 TTTATAGCAAAGGCATGGATCAAA 57.211 33.333 0.00 0.00 44.61 2.69
1671 1747 6.788598 TTTTATAGCAAAGGCATGGATCAA 57.211 33.333 0.00 0.00 44.61 2.57
1672 1748 6.788598 TTTTTATAGCAAAGGCATGGATCA 57.211 33.333 0.00 0.00 44.61 2.92
1827 1906 5.519927 GCAGGTTACAAAATGGCATTGTATC 59.480 40.000 14.47 12.38 41.46 2.24
1829 1908 4.526262 AGCAGGTTACAAAATGGCATTGTA 59.474 37.500 14.47 11.37 41.11 2.41
1855 1934 4.201724 GCTTACAAACGGCATAGTGAAGAG 60.202 45.833 0.00 0.00 0.00 2.85
1889 1968 4.141597 GGAGGGGAGGAGAGAAAACATTAG 60.142 50.000 0.00 0.00 0.00 1.73
1892 1971 2.200955 GGAGGGGAGGAGAGAAAACAT 58.799 52.381 0.00 0.00 0.00 2.71
1923 2002 1.880819 CTTTGGACATGGCCAGCACC 61.881 60.000 22.25 14.42 39.52 5.01
1927 2006 2.703798 CGGCTTTGGACATGGCCAG 61.704 63.158 22.25 11.82 44.27 4.85
1945 2024 2.288395 CCCACATGAAGCTTCCAACAAC 60.288 50.000 23.42 0.00 0.00 3.32
2152 2231 2.840753 GGAGGGTTGGCCACAGGAA 61.841 63.158 3.88 0.00 36.17 3.36
2241 2320 6.611613 AGTTCAGATGGAATTCTGTCACTA 57.388 37.500 5.23 0.00 43.02 2.74
2256 2338 2.767505 GAACCACGGTGAAGTTCAGAT 58.232 47.619 19.04 0.00 39.71 2.90
2270 2352 4.495422 ACATCTGATCAAGTACGAACCAC 58.505 43.478 0.00 0.00 0.00 4.16
2367 2449 1.304052 TTGGAACAGGCAATCCCCG 60.304 57.895 1.50 0.00 42.39 5.73
2376 2458 2.065899 TTGAACCCAGTTGGAACAGG 57.934 50.000 0.00 0.00 42.39 4.00
2426 2508 0.676466 ATTCCGTTGCTGGCGATTCA 60.676 50.000 0.00 0.00 0.00 2.57
2538 2620 1.689233 ATAGCCCGGCAGTCCTTCA 60.689 57.895 13.15 0.00 0.00 3.02
2628 2710 2.185004 AGGCCACATGGTAATATCGC 57.815 50.000 5.01 0.00 37.57 4.58
2722 2804 0.806102 GCAAGCTTCGCATAGACGGA 60.806 55.000 13.73 0.00 0.00 4.69
2730 2812 3.475566 AGGAATATAGCAAGCTTCGCA 57.524 42.857 18.74 8.65 0.00 5.10
2838 2920 0.252197 AGTCATGCATGAGCTCAGCA 59.748 50.000 30.01 30.01 42.74 4.41
2889 2971 4.082571 ACTTGGCTTATGAACATTGACAGC 60.083 41.667 0.00 0.00 0.00 4.40
2912 2994 2.890311 CAACCAAGTGCAGTCCCAATTA 59.110 45.455 0.00 0.00 0.00 1.40
2976 3058 0.034767 CTCCCAGATGCTCTTTGCCA 60.035 55.000 0.00 0.00 42.00 4.92
3103 3185 5.394562 AAGGCCATAAGGAAGAAAGCTAT 57.605 39.130 5.01 0.00 36.89 2.97
3161 3243 3.141767 AGTTACTTGCCTTCCACTTCC 57.858 47.619 0.00 0.00 0.00 3.46
3336 3418 1.341383 GCCCAAAGTCCATCTCCACAT 60.341 52.381 0.00 0.00 0.00 3.21
3948 4117 6.421801 GCATGCTTTTCTTTTTCTGTATGTGT 59.578 34.615 11.37 0.00 0.00 3.72
4044 4213 4.646040 TGGATAACAGCTGAAATTGATGGG 59.354 41.667 23.35 0.00 0.00 4.00
4164 4333 7.949434 ACACTCTTATATTAGTTTACGGAGGG 58.051 38.462 0.00 0.00 0.00 4.30
4165 4334 9.813446 AAACACTCTTATATTAGTTTACGGAGG 57.187 33.333 0.00 0.00 0.00 4.30
4213 4382 8.968969 CCCTCTGTAAACTACTATAAGAGTGTT 58.031 37.037 0.00 0.00 39.39 3.32
4214 4383 8.334734 TCCCTCTGTAAACTACTATAAGAGTGT 58.665 37.037 0.00 0.00 39.39 3.55
4215 4384 8.749026 TCCCTCTGTAAACTACTATAAGAGTG 57.251 38.462 0.00 0.00 39.39 3.51
4216 4385 8.559175 ACTCCCTCTGTAAACTACTATAAGAGT 58.441 37.037 0.00 0.00 42.69 3.24
4217 4386 8.983702 ACTCCCTCTGTAAACTACTATAAGAG 57.016 38.462 0.00 0.00 0.00 2.85
4218 4387 9.844257 GTACTCCCTCTGTAAACTACTATAAGA 57.156 37.037 0.00 0.00 0.00 2.10
4219 4388 8.772705 CGTACTCCCTCTGTAAACTACTATAAG 58.227 40.741 0.00 0.00 0.00 1.73
4220 4389 8.267894 ACGTACTCCCTCTGTAAACTACTATAA 58.732 37.037 0.00 0.00 0.00 0.98
4221 4390 7.796054 ACGTACTCCCTCTGTAAACTACTATA 58.204 38.462 0.00 0.00 0.00 1.31
4222 4391 6.657875 ACGTACTCCCTCTGTAAACTACTAT 58.342 40.000 0.00 0.00 0.00 2.12
4223 4392 6.054860 ACGTACTCCCTCTGTAAACTACTA 57.945 41.667 0.00 0.00 0.00 1.82
4224 4393 4.916183 ACGTACTCCCTCTGTAAACTACT 58.084 43.478 0.00 0.00 0.00 2.57
4225 4394 4.697352 TGACGTACTCCCTCTGTAAACTAC 59.303 45.833 0.00 0.00 0.00 2.73
4226 4395 4.910195 TGACGTACTCCCTCTGTAAACTA 58.090 43.478 0.00 0.00 0.00 2.24
4227 4396 3.759581 TGACGTACTCCCTCTGTAAACT 58.240 45.455 0.00 0.00 0.00 2.66
4228 4397 4.715527 ATGACGTACTCCCTCTGTAAAC 57.284 45.455 0.00 0.00 0.00 2.01
4229 4398 4.337555 GCTATGACGTACTCCCTCTGTAAA 59.662 45.833 0.00 0.00 0.00 2.01
4230 4399 3.881688 GCTATGACGTACTCCCTCTGTAA 59.118 47.826 0.00 0.00 0.00 2.41
4231 4400 3.474600 GCTATGACGTACTCCCTCTGTA 58.525 50.000 0.00 0.00 0.00 2.74
4232 4401 2.299521 GCTATGACGTACTCCCTCTGT 58.700 52.381 0.00 0.00 0.00 3.41
4233 4402 1.609555 GGCTATGACGTACTCCCTCTG 59.390 57.143 0.00 0.00 0.00 3.35
4234 4403 1.214673 TGGCTATGACGTACTCCCTCT 59.785 52.381 0.00 0.00 0.00 3.69
4235 4404 1.688772 TGGCTATGACGTACTCCCTC 58.311 55.000 0.00 0.00 0.00 4.30
4236 4405 2.154567 TTGGCTATGACGTACTCCCT 57.845 50.000 0.00 0.00 0.00 4.20
4237 4406 2.973694 TTTGGCTATGACGTACTCCC 57.026 50.000 0.00 0.00 0.00 4.30
4238 4407 3.793559 ACATTTGGCTATGACGTACTCC 58.206 45.455 7.09 0.00 0.00 3.85
4239 4408 6.897259 TTAACATTTGGCTATGACGTACTC 57.103 37.500 7.09 0.00 0.00 2.59
4240 4409 7.675962 TTTTAACATTTGGCTATGACGTACT 57.324 32.000 7.09 0.00 0.00 2.73
4359 4531 2.531522 AAATTGCAGGGCACTGTTTC 57.468 45.000 19.18 0.79 46.62 2.78


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

AutoCloner maintained by Alex Coulton.