Multiple sequence alignment - TraesCS1D01G266700

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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 TraesCS1D01G266700 chr1D 100.000 5934 0 0 1 5934 362493891 362487958 0.000000e+00 10959
1 TraesCS1D01G266700 chr1A 89.696 6056 305 139 1 5934 462005980 462000122 0.000000e+00 7432
2 TraesCS1D01G266700 chr1B 90.542 2823 123 69 3 2730 485293757 485290984 0.000000e+00 3602
3 TraesCS1D01G266700 chr1B 96.267 1661 47 4 3851 5504 485289761 485288109 0.000000e+00 2710
4 TraesCS1D01G266700 chr1B 95.634 733 31 1 2859 3590 485290832 485290100 0.000000e+00 1175
5 TraesCS1D01G266700 chr1B 95.592 431 19 0 5504 5934 485288051 485287621 0.000000e+00 691
6 TraesCS1D01G266700 chr1B 90.323 93 4 1 2774 2861 485290981 485290889 3.760000e-22 117
7 TraesCS1D01G266700 chr3A 85.759 962 135 2 3907 4867 653853001 653852041 0.000000e+00 1016
8 TraesCS1D01G266700 chr3B 85.343 962 139 2 3907 4867 682787559 682786599 0.000000e+00 994
9 TraesCS1D01G266700 chr3D 83.730 1051 158 8 3907 4949 518153052 518152007 0.000000e+00 981
10 TraesCS1D01G266700 chr5B 73.520 608 141 18 4142 4739 87979484 87978887 4.660000e-51 213
11 TraesCS1D01G266700 chr5D 73.311 607 143 17 4142 4739 78121095 78120499 7.800000e-49 206
12 TraesCS1D01G266700 chr5A 72.893 605 148 14 4142 4738 74679282 74678686 1.690000e-45 195


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 TraesCS1D01G266700 chr1D 362487958 362493891 5933 True 10959 10959 100.0000 1 5934 1 chr1D.!!$R1 5933
1 TraesCS1D01G266700 chr1A 462000122 462005980 5858 True 7432 7432 89.6960 1 5934 1 chr1A.!!$R1 5933
2 TraesCS1D01G266700 chr1B 485287621 485293757 6136 True 1659 3602 93.6716 3 5934 5 chr1B.!!$R1 5931
3 TraesCS1D01G266700 chr3A 653852041 653853001 960 True 1016 1016 85.7590 3907 4867 1 chr3A.!!$R1 960
4 TraesCS1D01G266700 chr3B 682786599 682787559 960 True 994 994 85.3430 3907 4867 1 chr3B.!!$R1 960
5 TraesCS1D01G266700 chr3D 518152007 518153052 1045 True 981 981 83.7300 3907 4949 1 chr3D.!!$R1 1042
6 TraesCS1D01G266700 chr5B 87978887 87979484 597 True 213 213 73.5200 4142 4739 1 chr5B.!!$R1 597
7 TraesCS1D01G266700 chr5D 78120499 78121095 596 True 206 206 73.3110 4142 4739 1 chr5D.!!$R1 597

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
512 539 0.174617 CTCCTCTTCCCGAGCAGAAC 59.825 60.000 0.00 0.0 38.49 3.01 F
629 656 0.322546 CAACCCCAACCCTCTGCTAC 60.323 60.000 0.00 0.0 0.00 3.58 F
717 757 0.753848 CTCTCGGTTCCCTCCCTCTC 60.754 65.000 0.00 0.0 0.00 3.20 F
1779 1905 0.884514 GTTTCTTTGGGCCTCTCTGC 59.115 55.000 4.53 0.0 0.00 4.26 F
2148 2290 0.740737 AGCTTGCGTTTGTGCTTCTT 59.259 45.000 0.00 0.0 35.36 2.52 F
2878 3095 0.250945 TTTGCCCGCCACTGATGTAA 60.251 50.000 0.00 0.0 0.00 2.41 F
3341 3558 1.004511 AGGCTTCATTTGCAGCTCTCT 59.995 47.619 2.38 0.0 34.71 3.10 F
4027 4366 1.377725 CCGGCAAGCAGGATCAACT 60.378 57.895 5.22 0.0 32.98 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1634 1756 0.752743 ATTGCCGATCACATGGGTGG 60.753 55.000 0.00 0.0 45.32 4.61 R
1699 1825 1.347221 GCCGACTCGTATTTTGCGG 59.653 57.895 0.00 0.0 41.51 5.69 R
1876 2002 2.647299 ACACATAACTGTCCCCATTGGA 59.353 45.455 3.62 0.0 42.41 3.53 R
2861 3017 0.958382 GTTTACATCAGTGGCGGGCA 60.958 55.000 0.00 0.0 0.00 5.36 R
3299 3516 2.229792 GCAACATCTCTTGACCAACCA 58.770 47.619 0.00 0.0 0.00 3.67 R
4324 4663 0.674581 TGCAGTTTGAGGGCTCGATG 60.675 55.000 0.00 0.0 0.00 3.84 R
4828 5167 0.679002 GCATGCTCTCCCAGAAGCAA 60.679 55.000 11.37 0.0 40.82 3.91 R
5734 6170 1.952296 CACATGCCCTGGAAATAGCTC 59.048 52.381 0.00 0.0 0.00 4.09 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
42 43 0.925267 CTTTTGCGTGAGTGCGTGTG 60.925 55.000 0.00 0.00 37.81 3.82
56 60 1.827681 CGTGTGGAGAGAGAAGAGGA 58.172 55.000 0.00 0.00 0.00 3.71
61 65 1.568597 TGGAGAGAGAAGAGGAGAGGG 59.431 57.143 0.00 0.00 0.00 4.30
167 181 4.021192 ACTCCTCTCTTGCTCTTCTTCTTG 60.021 45.833 0.00 0.00 0.00 3.02
196 210 6.096001 CCTTTCATTTGGTTCTGGATTCTAGG 59.904 42.308 0.00 0.00 0.00 3.02
200 214 3.121929 TGGTTCTGGATTCTAGGCTCT 57.878 47.619 0.00 0.00 0.00 4.09
273 287 2.159282 GCTCTTATCGTTCGGTTCTGGA 60.159 50.000 0.00 0.00 0.00 3.86
274 288 3.696898 CTCTTATCGTTCGGTTCTGGAG 58.303 50.000 0.00 0.00 0.00 3.86
275 289 2.426024 TCTTATCGTTCGGTTCTGGAGG 59.574 50.000 0.00 0.00 0.00 4.30
277 291 0.613853 ATCGTTCGGTTCTGGAGGGA 60.614 55.000 0.00 0.00 0.00 4.20
278 292 1.215647 CGTTCGGTTCTGGAGGGAG 59.784 63.158 0.00 0.00 0.00 4.30
280 294 1.157751 TTCGGTTCTGGAGGGAGGT 59.842 57.895 0.00 0.00 0.00 3.85
281 295 1.192146 TTCGGTTCTGGAGGGAGGTG 61.192 60.000 0.00 0.00 0.00 4.00
293 308 2.743928 GAGGTGCCTTCCGCTGTG 60.744 66.667 0.00 0.00 38.78 3.66
398 413 3.429085 GCATTTGCTTGATTCGATTCGT 58.571 40.909 5.89 0.00 38.21 3.85
399 414 3.479949 GCATTTGCTTGATTCGATTCGTC 59.520 43.478 5.89 0.00 38.21 4.20
401 416 1.277326 TGCTTGATTCGATTCGTCCG 58.723 50.000 5.89 0.00 0.00 4.79
402 417 1.278238 GCTTGATTCGATTCGTCCGT 58.722 50.000 5.89 0.00 0.00 4.69
403 418 1.255600 GCTTGATTCGATTCGTCCGTC 59.744 52.381 5.89 1.67 0.00 4.79
404 419 1.513178 CTTGATTCGATTCGTCCGTCG 59.487 52.381 5.89 0.00 39.11 5.12
405 420 0.448990 TGATTCGATTCGTCCGTCGT 59.551 50.000 5.89 0.00 40.80 4.34
406 421 1.135603 TGATTCGATTCGTCCGTCGTT 60.136 47.619 5.89 0.00 40.80 3.85
414 429 1.081376 CGTCCGTCGTTGCTCTCTT 60.081 57.895 0.00 0.00 34.52 2.85
457 476 2.157834 TTGTCAGTGGCGATTACGTT 57.842 45.000 0.00 0.00 41.98 3.99
460 479 2.873472 TGTCAGTGGCGATTACGTTTTT 59.127 40.909 0.00 0.00 41.98 1.94
486 508 3.076104 ATCAGCGGCAGTCTGATTG 57.924 52.632 14.50 0.00 45.99 2.67
490 512 0.250467 AGCGGCAGTCTGATTGTTGT 60.250 50.000 3.32 0.00 0.00 3.32
502 524 5.180304 GTCTGATTGTTGTTTCTCCTCTTCC 59.820 44.000 0.00 0.00 0.00 3.46
512 539 0.174617 CTCCTCTTCCCGAGCAGAAC 59.825 60.000 0.00 0.00 38.49 3.01
534 561 5.573146 ACAGAAAAGAAGAAGAAAACAGCG 58.427 37.500 0.00 0.00 0.00 5.18
583 610 3.352338 CTAGGCCGGGTCGTGTCAC 62.352 68.421 2.18 0.00 0.00 3.67
628 655 1.497309 CCAACCCCAACCCTCTGCTA 61.497 60.000 0.00 0.00 0.00 3.49
629 656 0.322546 CAACCCCAACCCTCTGCTAC 60.323 60.000 0.00 0.00 0.00 3.58
655 682 9.113838 CTCTGCTCTGCCTTCTATTTTATTTTA 57.886 33.333 0.00 0.00 0.00 1.52
717 757 0.753848 CTCTCGGTTCCCTCCCTCTC 60.754 65.000 0.00 0.00 0.00 3.20
719 759 2.231540 CTCGGTTCCCTCCCTCTCCT 62.232 65.000 0.00 0.00 0.00 3.69
723 763 1.550374 TTCCCTCCCTCTCCTCCCT 60.550 63.158 0.00 0.00 0.00 4.20
724 764 1.891296 TTCCCTCCCTCTCCTCCCTG 61.891 65.000 0.00 0.00 0.00 4.45
725 765 2.641746 CCCTCCCTCTCCTCCCTGT 61.642 68.421 0.00 0.00 0.00 4.00
728 768 2.443016 CCCTCTCCTCCCTGTCCG 60.443 72.222 0.00 0.00 0.00 4.79
729 769 2.360980 CCTCTCCTCCCTGTCCGT 59.639 66.667 0.00 0.00 0.00 4.69
730 770 1.755008 CCTCTCCTCCCTGTCCGTC 60.755 68.421 0.00 0.00 0.00 4.79
732 772 2.037367 CTCCTCCCTGTCCGTCCA 59.963 66.667 0.00 0.00 0.00 4.02
733 773 1.381872 CTCCTCCCTGTCCGTCCAT 60.382 63.158 0.00 0.00 0.00 3.41
734 774 1.680522 CTCCTCCCTGTCCGTCCATG 61.681 65.000 0.00 0.00 0.00 3.66
736 776 1.990060 CTCCCTGTCCGTCCATGGT 60.990 63.158 12.58 0.00 0.00 3.55
770 810 2.766313 TCGATGCCATGCCATTACTAC 58.234 47.619 0.00 0.00 0.00 2.73
771 811 2.368548 TCGATGCCATGCCATTACTACT 59.631 45.455 0.00 0.00 0.00 2.57
772 812 2.738846 CGATGCCATGCCATTACTACTC 59.261 50.000 0.00 0.00 0.00 2.59
773 813 3.555795 CGATGCCATGCCATTACTACTCT 60.556 47.826 0.00 0.00 0.00 3.24
855 904 1.349234 CGCGTCTGACATGACATTGA 58.651 50.000 8.73 0.00 36.82 2.57
890 939 2.355132 GCTGTGATTGCAGATGAGAAGG 59.645 50.000 0.00 0.00 38.70 3.46
1043 1096 2.504519 GGCCGCGTAAGATTCCCT 59.495 61.111 4.92 0.00 43.02 4.20
1069 1122 2.802792 GCCCGCCCCGTTTTAATC 59.197 61.111 0.00 0.00 0.00 1.75
1073 1126 1.478916 CCCGCCCCGTTTTAATCAATT 59.521 47.619 0.00 0.00 0.00 2.32
1080 1138 5.983118 GCCCCGTTTTAATCAATTAATCCAG 59.017 40.000 0.00 0.00 32.78 3.86
1270 1331 2.390938 CGCCTCGTAATCTCGCATTAA 58.609 47.619 0.00 0.00 0.00 1.40
1271 1332 2.405357 CGCCTCGTAATCTCGCATTAAG 59.595 50.000 0.00 0.00 0.00 1.85
1273 1334 3.670991 GCCTCGTAATCTCGCATTAAGAG 59.329 47.826 16.19 16.19 38.74 2.85
1274 1335 4.793353 GCCTCGTAATCTCGCATTAAGAGT 60.793 45.833 19.04 3.69 37.95 3.24
1275 1336 5.282510 CCTCGTAATCTCGCATTAAGAGTT 58.717 41.667 19.04 0.85 37.95 3.01
1276 1337 6.436261 CCTCGTAATCTCGCATTAAGAGTTA 58.564 40.000 19.04 0.17 37.95 2.24
1278 1339 7.024340 TCGTAATCTCGCATTAAGAGTTAGT 57.976 36.000 0.00 0.00 37.07 2.24
1279 1340 7.478322 TCGTAATCTCGCATTAAGAGTTAGTT 58.522 34.615 0.00 0.00 37.07 2.24
1280 1341 7.431376 TCGTAATCTCGCATTAAGAGTTAGTTG 59.569 37.037 0.00 0.00 37.07 3.16
1282 1343 4.181578 TCTCGCATTAAGAGTTAGTTGCC 58.818 43.478 0.00 0.00 37.07 4.52
1283 1344 3.267483 TCGCATTAAGAGTTAGTTGCCC 58.733 45.455 0.00 0.00 0.00 5.36
1284 1345 2.030457 CGCATTAAGAGTTAGTTGCCCG 59.970 50.000 0.00 0.00 0.00 6.13
1285 1346 3.267483 GCATTAAGAGTTAGTTGCCCGA 58.733 45.455 0.00 0.00 0.00 5.14
1286 1347 3.877508 GCATTAAGAGTTAGTTGCCCGAT 59.122 43.478 0.00 0.00 0.00 4.18
1290 1368 3.418684 AGAGTTAGTTGCCCGATGTTT 57.581 42.857 0.00 0.00 0.00 2.83
1292 1370 3.008049 AGAGTTAGTTGCCCGATGTTTCT 59.992 43.478 0.00 0.00 0.00 2.52
1311 1389 2.486966 GCATTGGCGGTGCTCTTC 59.513 61.111 6.66 0.00 39.45 2.87
1466 1585 3.160777 CTGATTTCAGCATCCTTTGGC 57.839 47.619 0.00 0.00 37.15 4.52
1479 1598 1.649664 CTTTGGCTCATCTCCTGTCG 58.350 55.000 0.00 0.00 0.00 4.35
1532 1654 1.625315 ACTAGTGTGCAAGGCTCATGA 59.375 47.619 0.00 0.00 34.62 3.07
1578 1700 2.112087 TGCGTACCAAGCAGCCAA 59.888 55.556 0.00 0.00 40.01 4.52
1619 1741 4.333649 TGATCCGATCAAAGATTTGTCAGC 59.666 41.667 8.70 0.00 39.18 4.26
1634 1756 3.399330 TGTCAGCTGTTAGGTACAAAGC 58.601 45.455 14.67 0.00 36.02 3.51
1699 1825 3.432890 CCTGAAAGATAGGGCTGGAGAAC 60.433 52.174 0.00 0.00 34.07 3.01
1779 1905 0.884514 GTTTCTTTGGGCCTCTCTGC 59.115 55.000 4.53 0.00 0.00 4.26
1783 1909 2.262774 CTTTGGGCCTCTCTGCGGAT 62.263 60.000 4.53 0.00 0.00 4.18
1845 1971 4.388773 GCGATCGGATATACTGCATTTTCA 59.611 41.667 18.30 0.00 0.00 2.69
1876 2002 2.193536 GGGCACACTTTTGGACGCT 61.194 57.895 0.00 0.00 0.00 5.07
1877 2003 1.282875 GGCACACTTTTGGACGCTC 59.717 57.895 0.00 0.00 0.00 5.03
1879 2005 1.444119 GCACACTTTTGGACGCTCCA 61.444 55.000 3.02 3.02 46.61 3.86
2010 2136 6.038997 ACCTGTATATAAAAGGATCGCCTC 57.961 41.667 16.27 0.00 46.28 4.70
2011 2137 5.046520 ACCTGTATATAAAAGGATCGCCTCC 60.047 44.000 16.27 0.00 46.28 4.30
2043 2179 3.788227 TTAAGAAGAAAGCAGGAGCCA 57.212 42.857 0.00 0.00 43.56 4.75
2048 2184 2.664402 AGAAAGCAGGAGCCAGAAAA 57.336 45.000 0.00 0.00 43.56 2.29
2054 2190 1.615392 GCAGGAGCCAGAAAATGTTGT 59.385 47.619 0.00 0.00 33.58 3.32
2060 2196 4.984785 GGAGCCAGAAAATGTTGTTTTCTC 59.015 41.667 11.61 4.12 44.30 2.87
2069 2205 5.767816 AATGTTGTTTTCTCCTGGTGTAC 57.232 39.130 0.00 0.00 0.00 2.90
2148 2290 0.740737 AGCTTGCGTTTGTGCTTCTT 59.259 45.000 0.00 0.00 35.36 2.52
2149 2291 0.848305 GCTTGCGTTTGTGCTTCTTG 59.152 50.000 0.00 0.00 35.36 3.02
2324 2471 6.620877 ACTTAGGAACATCATAACCTGTCA 57.379 37.500 0.00 0.00 34.42 3.58
2389 2537 9.846248 CCAACCTAAGAATATTTTTCTTCTGTG 57.154 33.333 5.52 2.22 39.30 3.66
2404 2553 8.647143 TTTCTTCTGTGCTTTTTCCTATTTTG 57.353 30.769 0.00 0.00 0.00 2.44
2431 2580 4.883083 AGCATAGTTCTTTCGTGTCAGAA 58.117 39.130 0.00 0.00 0.00 3.02
2532 2681 7.148423 ACCAAAAGCAAAAGTTTCAAAGATGTC 60.148 33.333 0.00 0.00 0.00 3.06
2740 2889 3.743911 TGCGACACGTTAAAAGATGACAT 59.256 39.130 0.00 0.00 0.00 3.06
2744 2893 5.284424 CGACACGTTAAAAGATGACATACGA 59.716 40.000 11.93 0.00 0.00 3.43
2834 2990 7.961326 ATGAAGAAATTTTACTATGCAGGGT 57.039 32.000 0.00 0.00 0.00 4.34
2878 3095 0.250945 TTTGCCCGCCACTGATGTAA 60.251 50.000 0.00 0.00 0.00 2.41
2966 3183 2.622942 GGACAAAACAAGTGCTGATCCA 59.377 45.455 0.00 0.00 0.00 3.41
2972 3189 3.827008 ACAAGTGCTGATCCACGATAT 57.173 42.857 0.00 0.00 40.59 1.63
2981 3198 5.046529 GCTGATCCACGATATGTATCATCC 58.953 45.833 0.00 0.00 32.98 3.51
3218 3435 5.365314 GGAAGAATCTGAGATACCTTCCTGT 59.635 44.000 29.69 3.93 43.67 4.00
3254 3471 1.209275 CTAATGTCCGAAGAGGCGCG 61.209 60.000 0.00 0.00 40.77 6.86
3308 3525 2.391130 AAGGGTGGCTGGTTGGTCA 61.391 57.895 0.00 0.00 0.00 4.02
3341 3558 1.004511 AGGCTTCATTTGCAGCTCTCT 59.995 47.619 2.38 0.00 34.71 3.10
3452 3669 1.610522 CCCTGCAAGAACCTTGTGAAG 59.389 52.381 8.29 4.59 34.07 3.02
3503 3720 4.397417 CCTGATTTGAAAGCAGTAAGGGAG 59.603 45.833 20.13 1.30 43.15 4.30
3610 3827 1.399727 CGTTTCTCATTTCCGTGCACC 60.400 52.381 12.15 0.00 0.00 5.01
3628 3845 4.707448 TGCACCTGTTCTTCTTTAAAACCA 59.293 37.500 0.00 0.00 0.00 3.67
3651 3868 9.797642 ACCAATTAAGATATGCATATCAAGTGA 57.202 29.630 36.32 22.80 41.21 3.41
3657 3874 7.789202 AGATATGCATATCAAGTGACCTAGT 57.211 36.000 36.32 16.76 41.21 2.57
3658 3875 8.885693 AGATATGCATATCAAGTGACCTAGTA 57.114 34.615 36.32 3.12 41.21 1.82
3659 3876 9.486123 AGATATGCATATCAAGTGACCTAGTAT 57.514 33.333 36.32 16.24 41.21 2.12
3662 3879 8.657387 ATGCATATCAAGTGACCTAGTATAGT 57.343 34.615 0.00 0.00 36.82 2.12
3663 3880 9.755122 ATGCATATCAAGTGACCTAGTATAGTA 57.245 33.333 0.00 0.00 36.82 1.82
3664 3881 9.582648 TGCATATCAAGTGACCTAGTATAGTAA 57.417 33.333 0.00 0.00 36.82 2.24
3672 3889 9.509956 AAGTGACCTAGTATAGTAATGCTCTAG 57.490 37.037 0.00 0.00 36.82 2.43
3690 3907 6.491745 TGCTCTAGAAAGATGATACCCAGTAG 59.508 42.308 0.00 0.00 0.00 2.57
3696 3913 8.840200 AGAAAGATGATACCCAGTAGAACTAA 57.160 34.615 0.00 0.00 0.00 2.24
3705 3922 5.491982 ACCCAGTAGAACTAATTTCAGCAG 58.508 41.667 0.00 0.00 36.57 4.24
3721 3938 7.870509 TTTCAGCAGAAATAGCATCTAATGT 57.129 32.000 0.00 0.00 38.76 2.71
3741 3958 3.616821 TGTTGTCAGAGAAGTTCAACACG 59.383 43.478 5.50 0.00 41.77 4.49
3744 3961 5.001237 TGTCAGAGAAGTTCAACACGTTA 57.999 39.130 5.50 0.00 0.00 3.18
3746 3963 5.870433 TGTCAGAGAAGTTCAACACGTTAAA 59.130 36.000 5.50 0.00 0.00 1.52
3800 4017 6.556639 TCTCTAGGAATGCATATAGAGTGGT 58.443 40.000 26.68 3.20 41.24 4.16
3809 4026 6.747414 TGCATATAGAGTGGTCCTTGTTAT 57.253 37.500 0.00 0.00 0.00 1.89
3853 4087 4.601406 ATGGGCCCTGTTAGATTTTACA 57.399 40.909 25.70 0.00 0.00 2.41
4027 4366 1.377725 CCGGCAAGCAGGATCAACT 60.378 57.895 5.22 0.00 32.98 3.16
4324 4663 2.100631 CAACTCCGGCGTCATGGTC 61.101 63.158 6.01 0.00 0.00 4.02
4828 5167 3.134458 CAAGACCTGCTTCGAGAAGTTT 58.866 45.455 13.58 0.00 40.45 2.66
4887 5229 2.672478 CGAAGAACCAGACGAAGAGCAT 60.672 50.000 0.00 0.00 0.00 3.79
4924 5266 0.733909 CTGCGACGATGAGCTTGTCA 60.734 55.000 0.00 0.00 38.06 3.58
4925 5267 0.319469 TGCGACGATGAGCTTGTCAA 60.319 50.000 0.00 0.00 39.19 3.18
4926 5268 0.368227 GCGACGATGAGCTTGTCAAG 59.632 55.000 8.31 8.31 39.19 3.02
4927 5269 1.702886 CGACGATGAGCTTGTCAAGT 58.297 50.000 14.03 1.29 39.19 3.16
5093 5441 2.187424 CTCCTGGCTGCAGCTCTC 59.813 66.667 35.82 21.24 41.70 3.20
5094 5442 2.605601 TCCTGGCTGCAGCTCTCA 60.606 61.111 35.82 24.50 41.70 3.27
5095 5443 1.973816 CTCCTGGCTGCAGCTCTCAT 61.974 60.000 35.82 0.00 41.70 2.90
5096 5444 1.524165 CCTGGCTGCAGCTCTCATC 60.524 63.158 35.82 19.78 41.70 2.92
5097 5445 1.523046 CTGGCTGCAGCTCTCATCT 59.477 57.895 35.82 0.00 41.70 2.90
5098 5446 0.812014 CTGGCTGCAGCTCTCATCTG 60.812 60.000 35.82 18.66 41.70 2.90
5099 5447 1.524165 GGCTGCAGCTCTCATCTGG 60.524 63.158 35.82 0.00 41.70 3.86
5100 5448 2.181521 GCTGCAGCTCTCATCTGGC 61.182 63.158 31.33 0.18 38.21 4.85
5109 5457 1.203441 TCTCATCTGGCAGCCTTGGT 61.203 55.000 14.15 0.00 0.00 3.67
5251 5607 5.566469 TCTCCCGTTCCAAATTATTGAAGT 58.434 37.500 0.00 0.00 38.94 3.01
5442 5805 7.010183 CCGTGTCCAGAATTTAACTATGTACAG 59.990 40.741 0.33 0.00 0.00 2.74
5488 5860 2.041244 GGTACAAACTTTTTGCGCTCG 58.959 47.619 9.73 0.00 0.00 5.03
5491 5863 1.131504 ACAAACTTTTTGCGCTCGTCA 59.868 42.857 9.73 0.00 0.00 4.35
5634 6068 5.084722 GTGATGCTTTCTTTTCATCGACAG 58.915 41.667 0.00 0.00 39.42 3.51
5723 6159 2.173782 TGCAGAGGTCCAGTTAAACCAA 59.826 45.455 0.00 0.00 38.06 3.67
5734 6170 7.280205 GGTCCAGTTAAACCAACTATCATACTG 59.720 40.741 0.00 0.00 46.04 2.74
5752 6188 2.228059 CTGAGCTATTTCCAGGGCATG 58.772 52.381 0.00 0.00 0.00 4.06
5799 6238 3.181483 ACCGAAGATGGGAATGTACGTAC 60.181 47.826 18.90 18.90 0.00 3.67
5811 6250 1.070821 GTACGTACGGGGCAAAAGAC 58.929 55.000 21.06 0.00 0.00 3.01
5853 6292 1.948611 GCCATCTTTCGCCAACCTGTA 60.949 52.381 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 1.133482 CCCCTCTCCTCTTCTCTCTCC 60.133 61.905 0.00 0.00 0.00 3.71
61 65 2.815647 CGAGAAACGGGCTGCTCC 60.816 66.667 0.00 0.00 38.46 4.70
167 181 2.232208 CCAGAACCAAATGAAAGGAGCC 59.768 50.000 0.00 0.00 0.00 4.70
200 214 2.032528 CCAAGAGCAACTCCGCCA 59.967 61.111 0.00 0.00 0.00 5.69
281 295 2.820037 GCTACCACAGCGGAAGGC 60.820 66.667 0.00 0.00 41.37 4.35
293 308 1.298859 CCAGCACCAACGAAGCTACC 61.299 60.000 0.00 0.00 36.73 3.18
393 408 0.456312 GAGAGCAACGACGGACGAAT 60.456 55.000 6.90 0.00 45.77 3.34
394 409 1.081641 GAGAGCAACGACGGACGAA 60.082 57.895 6.90 0.00 45.77 3.85
397 412 1.061485 GAAAGAGAGCAACGACGGAC 58.939 55.000 0.00 0.00 0.00 4.79
398 413 0.959553 AGAAAGAGAGCAACGACGGA 59.040 50.000 0.00 0.00 0.00 4.69
399 414 1.784525 AAGAAAGAGAGCAACGACGG 58.215 50.000 0.00 0.00 0.00 4.79
401 416 5.411083 AAAGAAAGAAAGAGAGCAACGAC 57.589 39.130 0.00 0.00 0.00 4.34
402 417 6.436843 AAAAAGAAAGAAAGAGAGCAACGA 57.563 33.333 0.00 0.00 0.00 3.85
442 461 2.492001 CGAAAAACGTAATCGCCACTG 58.508 47.619 4.90 0.00 41.18 3.66
485 507 2.037251 CTCGGGAAGAGGAGAAACAACA 59.963 50.000 0.00 0.00 43.20 3.33
486 508 2.689646 CTCGGGAAGAGGAGAAACAAC 58.310 52.381 0.00 0.00 43.20 3.32
490 512 3.067011 TGCTCGGGAAGAGGAGAAA 57.933 52.632 0.00 0.00 46.91 2.52
502 524 3.393800 TCTTCTTTTCTGTTCTGCTCGG 58.606 45.455 0.00 0.00 0.00 4.63
512 539 4.972440 CCGCTGTTTTCTTCTTCTTTTCTG 59.028 41.667 0.00 0.00 0.00 3.02
534 561 6.806739 CAGGGAAACAATAAAGAAAACGATCC 59.193 38.462 0.00 0.00 0.00 3.36
618 645 0.334676 AGAGCAGAGTAGCAGAGGGT 59.665 55.000 0.00 0.00 36.85 4.34
628 655 4.566426 AAAATAGAAGGCAGAGCAGAGT 57.434 40.909 0.00 0.00 0.00 3.24
629 656 7.565323 AAATAAAATAGAAGGCAGAGCAGAG 57.435 36.000 0.00 0.00 0.00 3.35
717 757 2.735772 CCATGGACGGACAGGGAGG 61.736 68.421 5.56 0.00 44.73 4.30
719 759 2.121832 ACCATGGACGGACAGGGA 59.878 61.111 21.47 0.00 44.73 4.20
723 763 1.070615 CACACACCATGGACGGACA 59.929 57.895 21.47 0.00 0.00 4.02
724 764 1.070786 ACACACACCATGGACGGAC 59.929 57.895 21.47 0.00 0.00 4.79
725 765 1.070615 CACACACACCATGGACGGA 59.929 57.895 21.47 0.00 0.00 4.69
728 768 1.065401 CAACACACACACACCATGGAC 59.935 52.381 21.47 0.00 0.00 4.02
729 769 1.065126 TCAACACACACACACCATGGA 60.065 47.619 21.47 0.00 0.00 3.41
730 770 1.387539 TCAACACACACACACCATGG 58.612 50.000 11.19 11.19 0.00 3.66
732 772 1.872952 CGATCAACACACACACACCAT 59.127 47.619 0.00 0.00 0.00 3.55
733 773 1.134670 TCGATCAACACACACACACCA 60.135 47.619 0.00 0.00 0.00 4.17
734 774 1.577468 TCGATCAACACACACACACC 58.423 50.000 0.00 0.00 0.00 4.16
736 776 1.530720 GCATCGATCAACACACACACA 59.469 47.619 0.00 0.00 0.00 3.72
770 810 2.158608 GGAGGGGAAGAGAGAGAGAGAG 60.159 59.091 0.00 0.00 0.00 3.20
771 811 1.850345 GGAGGGGAAGAGAGAGAGAGA 59.150 57.143 0.00 0.00 0.00 3.10
772 812 1.568597 TGGAGGGGAAGAGAGAGAGAG 59.431 57.143 0.00 0.00 0.00 3.20
773 813 1.687492 TGGAGGGGAAGAGAGAGAGA 58.313 55.000 0.00 0.00 0.00 3.10
855 904 0.466189 CACAGCAACAGAACAGGGGT 60.466 55.000 0.00 0.00 0.00 4.95
1069 1122 5.444176 AGGGAAAGAGCTCTGGATTAATTG 58.556 41.667 19.06 0.00 0.00 2.32
1073 1126 5.251700 AGAAAAGGGAAAGAGCTCTGGATTA 59.748 40.000 19.06 0.00 0.00 1.75
1080 1138 3.046968 ACGAGAAAAGGGAAAGAGCTC 57.953 47.619 5.27 5.27 0.00 4.09
1196 1254 1.550072 GCAGCAATAAAAGGGGAAGCA 59.450 47.619 0.00 0.00 0.00 3.91
1253 1314 7.133513 ACTAACTCTTAATGCGAGATTACGAG 58.866 38.462 14.47 14.47 36.52 4.18
1270 1331 3.008049 AGAAACATCGGGCAACTAACTCT 59.992 43.478 0.00 0.00 0.00 3.24
1271 1332 3.335579 AGAAACATCGGGCAACTAACTC 58.664 45.455 0.00 0.00 0.00 3.01
1273 1334 2.093783 CGAGAAACATCGGGCAACTAAC 59.906 50.000 0.00 0.00 39.04 2.34
1274 1335 2.343101 CGAGAAACATCGGGCAACTAA 58.657 47.619 0.00 0.00 39.04 2.24
1275 1336 2.004583 CGAGAAACATCGGGCAACTA 57.995 50.000 0.00 0.00 39.04 2.24
1276 1337 1.298859 GCGAGAAACATCGGGCAACT 61.299 55.000 0.00 0.00 42.94 3.16
1278 1339 0.676466 ATGCGAGAAACATCGGGCAA 60.676 50.000 0.00 0.00 42.94 4.52
1279 1340 0.676466 AATGCGAGAAACATCGGGCA 60.676 50.000 0.00 0.00 42.94 5.36
1280 1341 0.248215 CAATGCGAGAAACATCGGGC 60.248 55.000 0.00 0.00 42.94 6.13
1282 1343 0.248215 GCCAATGCGAGAAACATCGG 60.248 55.000 0.00 0.00 42.94 4.18
1283 1344 3.224955 GCCAATGCGAGAAACATCG 57.775 52.632 0.00 0.00 45.48 3.84
1306 1384 2.069430 GGCTCAGGGAGGGGAAGAG 61.069 68.421 0.00 0.00 0.00 2.85
1463 1582 1.305297 ACCGACAGGAGATGAGCCA 60.305 57.895 0.00 0.00 41.02 4.75
1466 1585 1.756430 TCAGACCGACAGGAGATGAG 58.244 55.000 0.00 0.00 41.02 2.90
1479 1598 6.625873 AAAATGAAGTTCAGAGTTCAGACC 57.374 37.500 11.91 0.00 45.66 3.85
1532 1654 3.299503 AGCACAACTTGGAACCTTCATT 58.700 40.909 0.00 0.00 0.00 2.57
1571 1693 2.575461 GGAAGCATGGTTGGCTGC 59.425 61.111 16.18 0.00 41.66 5.25
1578 1700 3.173953 TCAAATTCAGGGAAGCATGGT 57.826 42.857 0.00 0.00 0.00 3.55
1619 1741 2.224670 TGGGTGGCTTTGTACCTAACAG 60.225 50.000 0.00 0.00 39.87 3.16
1634 1756 0.752743 ATTGCCGATCACATGGGTGG 60.753 55.000 0.00 0.00 45.32 4.61
1699 1825 1.347221 GCCGACTCGTATTTTGCGG 59.653 57.895 0.00 0.00 41.51 5.69
1876 2002 2.647299 ACACATAACTGTCCCCATTGGA 59.353 45.455 3.62 0.00 42.41 3.53
1877 2003 3.085952 ACACATAACTGTCCCCATTGG 57.914 47.619 0.00 0.00 31.62 3.16
1879 2005 7.790782 AAAAATACACATAACTGTCCCCATT 57.209 32.000 0.00 0.00 31.62 3.16
2002 2128 5.652994 AATAATCAGTAGAGGAGGCGATC 57.347 43.478 0.00 0.00 0.00 3.69
2010 2136 9.823647 TGCTTTCTTCTTAATAATCAGTAGAGG 57.176 33.333 0.00 0.00 0.00 3.69
2016 2142 7.255070 GGCTCCTGCTTTCTTCTTAATAATCAG 60.255 40.741 0.00 0.00 39.59 2.90
2017 2143 6.543831 GGCTCCTGCTTTCTTCTTAATAATCA 59.456 38.462 0.00 0.00 39.59 2.57
2018 2144 6.543831 TGGCTCCTGCTTTCTTCTTAATAATC 59.456 38.462 0.00 0.00 39.59 1.75
2048 2184 4.141251 AGGTACACCAGGAGAAAACAACAT 60.141 41.667 0.38 0.00 38.89 2.71
2054 2190 3.201266 ACAACAGGTACACCAGGAGAAAA 59.799 43.478 0.38 0.00 38.89 2.29
2060 2196 2.838202 AGGATACAACAGGTACACCAGG 59.162 50.000 0.38 0.00 37.56 4.45
2307 2454 6.741992 TTGACATGACAGGTTATGATGTTC 57.258 37.500 10.68 0.00 29.08 3.18
2389 2537 5.845985 GCTTGTCCAAAATAGGAAAAAGC 57.154 39.130 12.87 12.87 45.01 3.51
2399 2548 6.016276 ACGAAAGAACTATGCTTGTCCAAAAT 60.016 34.615 0.00 0.00 0.00 1.82
2404 2553 3.746492 ACACGAAAGAACTATGCTTGTCC 59.254 43.478 0.00 0.00 0.00 4.02
2461 2610 9.197694 GTCATCACTGCATAAGGTAGTAATAAG 57.802 37.037 0.00 0.00 40.80 1.73
2661 2810 3.585862 TCACCGAGAACTTGATTGTAGC 58.414 45.455 0.00 0.00 0.00 3.58
2740 2889 3.552068 CGCCACTGGAATACATCATCGTA 60.552 47.826 0.00 0.00 0.00 3.43
2744 2893 1.768275 TCCGCCACTGGAATACATCAT 59.232 47.619 0.00 0.00 34.30 2.45
2752 2901 1.596934 CTAAGCTCCGCCACTGGAA 59.403 57.895 0.00 0.00 37.64 3.53
2753 2902 3.019003 GCTAAGCTCCGCCACTGGA 62.019 63.158 0.00 0.00 36.37 3.86
2861 3017 0.958382 GTTTACATCAGTGGCGGGCA 60.958 55.000 0.00 0.00 0.00 5.36
3126 3343 3.054139 TCCTTGGCATGCTCAAGTCTTAT 60.054 43.478 30.31 0.00 39.78 1.73
3218 3435 4.166725 ACATTAGGCTCTGGAAATGATGGA 59.833 41.667 12.60 0.00 34.26 3.41
3254 3471 5.119931 TCACAGCAATAACATCAAACCAC 57.880 39.130 0.00 0.00 0.00 4.16
3299 3516 2.229792 GCAACATCTCTTGACCAACCA 58.770 47.619 0.00 0.00 0.00 3.67
3308 3525 2.867624 TGAAGCCTTGCAACATCTCTT 58.132 42.857 0.00 0.00 0.00 2.85
3467 3684 5.186256 TCAAATCAGGCCTATACAACCAA 57.814 39.130 3.98 0.00 0.00 3.67
3642 3859 9.809395 AGCATTACTATACTAGGTCACTTGATA 57.191 33.333 0.00 0.00 0.00 2.15
3647 3864 8.882282 TCTAGAGCATTACTATACTAGGTCACT 58.118 37.037 0.00 0.00 0.00 3.41
3648 3865 9.504708 TTCTAGAGCATTACTATACTAGGTCAC 57.495 37.037 0.00 0.00 0.00 3.67
3659 3876 9.026121 GGGTATCATCTTTCTAGAGCATTACTA 57.974 37.037 0.00 0.00 32.92 1.82
3660 3877 7.510685 TGGGTATCATCTTTCTAGAGCATTACT 59.489 37.037 0.00 0.00 32.92 2.24
3661 3878 7.671302 TGGGTATCATCTTTCTAGAGCATTAC 58.329 38.462 0.00 0.00 32.92 1.89
3662 3879 7.510685 ACTGGGTATCATCTTTCTAGAGCATTA 59.489 37.037 0.00 0.00 32.92 1.90
3663 3880 6.328672 ACTGGGTATCATCTTTCTAGAGCATT 59.671 38.462 0.00 0.00 32.92 3.56
3664 3881 5.843421 ACTGGGTATCATCTTTCTAGAGCAT 59.157 40.000 0.00 0.00 32.92 3.79
3676 3893 9.482627 CTGAAATTAGTTCTACTGGGTATCATC 57.517 37.037 0.00 0.00 37.13 2.92
3705 3922 8.654230 TCTCTGACAACATTAGATGCTATTTC 57.346 34.615 0.00 0.00 0.00 2.17
3720 3937 3.617263 ACGTGTTGAACTTCTCTGACAAC 59.383 43.478 0.00 0.00 40.44 3.32
3721 3938 3.857052 ACGTGTTGAACTTCTCTGACAA 58.143 40.909 0.00 0.00 0.00 3.18
3762 3979 9.080097 GCATTCCTAGAGAATAGACCTTAGTAA 57.920 37.037 6.24 0.00 43.63 2.24
4027 4366 4.847512 TCAACAAGGATAACCAAGTCCCTA 59.152 41.667 0.00 0.00 38.94 3.53
4324 4663 0.674581 TGCAGTTTGAGGGCTCGATG 60.675 55.000 0.00 0.00 0.00 3.84
4372 4711 1.135888 CCGTTGTACGACGTGATCTCA 60.136 52.381 28.97 0.00 46.05 3.27
4414 4753 3.544684 GTGCCACCATGTGAATATCTCA 58.455 45.455 0.00 0.00 35.23 3.27
4828 5167 0.679002 GCATGCTCTCCCAGAAGCAA 60.679 55.000 11.37 0.00 40.82 3.91
4924 5266 3.944055 ATCTACACAGCTCACGAACTT 57.056 42.857 0.00 0.00 0.00 2.66
4925 5267 3.181495 GCTATCTACACAGCTCACGAACT 60.181 47.826 0.00 0.00 34.86 3.01
4926 5268 3.109619 GCTATCTACACAGCTCACGAAC 58.890 50.000 0.00 0.00 34.86 3.95
4927 5269 2.099263 GGCTATCTACACAGCTCACGAA 59.901 50.000 0.00 0.00 37.91 3.85
5093 5441 2.050350 CCACCAAGGCTGCCAGATG 61.050 63.158 22.65 15.85 0.00 2.90
5094 5442 2.357836 CCACCAAGGCTGCCAGAT 59.642 61.111 22.65 3.39 0.00 2.90
5095 5443 3.177884 ACCACCAAGGCTGCCAGA 61.178 61.111 22.65 0.00 43.14 3.86
5096 5444 2.987547 CACCACCAAGGCTGCCAG 60.988 66.667 22.65 12.76 43.14 4.85
5097 5445 4.601794 CCACCACCAAGGCTGCCA 62.602 66.667 22.65 0.00 43.14 4.92
5109 5457 2.158842 CCAAAAGAATTGTTGGCCACCA 60.159 45.455 3.88 0.00 38.04 4.17
5410 5766 7.838771 AGTTAAATTCTGGACACGGTATAAC 57.161 36.000 0.00 0.00 0.00 1.89
5512 5946 8.974408 GCTCACATCACACGTTGTATAAATATA 58.026 33.333 0.00 0.00 0.00 0.86
5513 5947 7.710907 AGCTCACATCACACGTTGTATAAATAT 59.289 33.333 0.00 0.00 0.00 1.28
5514 5948 7.010091 CAGCTCACATCACACGTTGTATAAATA 59.990 37.037 0.00 0.00 0.00 1.40
5515 5949 5.874810 AGCTCACATCACACGTTGTATAAAT 59.125 36.000 0.00 0.00 0.00 1.40
5525 5959 2.677199 ACTAACAGCTCACATCACACG 58.323 47.619 0.00 0.00 0.00 4.49
5537 5971 5.517054 GCTTCAGTCTGTATGTACTAACAGC 59.483 44.000 18.06 14.27 42.31 4.40
5590 6024 3.737266 ACATTTTGTGCATGCTTCTTTCG 59.263 39.130 20.33 5.48 0.00 3.46
5634 6068 5.420409 AGATTTTGTATCGGTCCTTCAGAC 58.580 41.667 0.00 0.00 45.51 3.51
5734 6170 1.952296 CACATGCCCTGGAAATAGCTC 59.048 52.381 0.00 0.00 0.00 4.09
5752 6188 4.748892 TGTCAGCTATAGAAGAGCAACAC 58.251 43.478 3.21 0.00 42.69 3.32
5799 6238 3.949031 TTTTTCGTCTTTTGCCCCG 57.051 47.368 0.00 0.00 0.00 5.73
5853 6292 6.537355 TGACCTTTCTTCATGTCTGAAATCT 58.463 36.000 9.55 1.72 40.78 2.40


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

AutoCloner maintained by Alex Coulton.