Multiple sequence alignment - TraesCS1D01G372200

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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 TraesCS1D01G372200 chr1D 100.000 7980 0 0 1 7980 450217058 450225037 0.000000e+00 14737.0
1 TraesCS1D01G372200 chr1D 92.000 75 5 1 5439 5513 450222430 450222503 3.940000e-18 104.0
2 TraesCS1D01G372200 chr1D 92.000 75 5 1 5373 5446 450222496 450222570 3.940000e-18 104.0
3 TraesCS1D01G372200 chr1A 93.283 4198 145 55 583 4690 545521052 545525202 0.000000e+00 6063.0
4 TraesCS1D01G372200 chr1A 93.076 2614 109 29 5373 7980 545525993 545528540 0.000000e+00 3759.0
5 TraesCS1D01G372200 chr1A 93.254 845 25 14 4687 5513 545525236 545526066 0.000000e+00 1216.0
6 TraesCS1D01G372200 chr1A 87.879 363 24 12 1 354 545519973 545520324 7.450000e-110 409.0
7 TraesCS1D01G372200 chr1A 95.062 81 1 2 5433 5513 545525923 545526000 3.020000e-24 124.0
8 TraesCS1D01G372200 chr1A 96.825 63 1 1 5385 5446 545526071 545526133 3.940000e-18 104.0
9 TraesCS1D01G372200 chr1A 100.000 29 0 0 7653 7681 545527249 545527277 4.000000e-03 54.7
10 TraesCS1D01G372200 chr1B 94.807 2850 83 22 1898 4690 617817858 617820699 0.000000e+00 4383.0
11 TraesCS1D01G372200 chr1B 95.630 1945 55 13 5373 7308 617821494 617823417 0.000000e+00 3094.0
12 TraesCS1D01G372200 chr1B 87.410 1938 136 51 1 1861 617815952 617817858 0.000000e+00 2128.0
13 TraesCS1D01G372200 chr1B 94.251 835 24 9 4697 5513 617820739 617821567 0.000000e+00 1254.0
14 TraesCS1D01G372200 chr1B 86.180 644 59 13 7345 7980 617823420 617824041 0.000000e+00 669.0
15 TraesCS1D01G372200 chr1B 92.593 81 3 2 5433 5513 617821424 617821501 6.550000e-21 113.0
16 TraesCS1D01G372200 chr1B 93.333 75 4 1 5373 5446 617821560 617821634 8.470000e-20 110.0
17 TraesCS1D01G372200 chr3A 75.792 442 91 9 4940 5378 67556340 67556768 8.110000e-50 209.0
18 TraesCS1D01G372200 chr3A 75.339 442 93 9 4940 5378 67527737 67528165 1.760000e-46 198.0
19 TraesCS1D01G372200 chr3D 87.342 79 1 4 4612 4689 58559168 58559238 1.850000e-11 82.4


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 TraesCS1D01G372200 chr1D 450217058 450225037 7979 False 4981.666667 14737 94.666667 1 7980 3 chr1D.!!$F1 7979
1 TraesCS1D01G372200 chr1A 545519973 545528540 8567 False 1675.671429 6063 94.197000 1 7980 7 chr1A.!!$F1 7979
2 TraesCS1D01G372200 chr1B 617815952 617824041 8089 False 1678.714286 4383 92.029143 1 7980 7 chr1B.!!$F1 7979

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
435 569 0.666913 CCTACGTACGGATGGTCTGG 59.333 60.000 21.06 3.23 0.00 3.86 F
1235 1789 0.391793 GCGCCTGGAAGTAAGAAGCT 60.392 55.000 0.00 0.00 0.00 3.74 F
2076 2689 0.039708 GTGCAAGGTTCTTGCTGCTC 60.040 55.000 26.22 14.17 45.13 4.26 F
2698 3327 0.774491 AGCCCCACCTTAGGAAACCA 60.774 55.000 4.77 0.00 0.00 3.67 F
4092 4740 0.960364 CACACTGCTATTTGCCGGGT 60.960 55.000 2.18 0.00 43.32 5.28 F
5788 6567 0.820871 CCAGAGCTAGTCCAGTGTCC 59.179 60.000 0.00 0.00 0.00 4.02 F
6275 7062 1.338769 CGAAGGAATTCGGACCTTGGT 60.339 52.381 0.00 0.00 45.08 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1258 1831 0.110238 CACGCTCCAACACCGAATTG 60.110 55.000 0.00 0.0 0.00 2.32 R
2715 3344 1.208052 GCCTCTTGAGCACACATAGGA 59.792 52.381 9.04 0.0 0.00 2.94 R
3479 4112 1.149174 GTGGCCCGACATCCATCAT 59.851 57.895 0.00 0.0 34.47 2.45 R
4207 4855 0.179073 CGCTGTGGCCTAGCATAACT 60.179 55.000 25.36 0.0 41.18 2.24 R
5833 6612 1.001378 CAACTTGACAAGGGCTTTCCG 60.001 52.381 19.16 0.0 41.52 4.30 R
6751 7538 0.962489 CGTAGAGGGCCTGTAGATGG 59.038 60.000 12.95 0.0 0.00 3.51 R
7843 8656 0.396060 GCCCAAGCCAAATCAACCAA 59.604 50.000 0.00 0.0 0.00 3.67 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
29 30 3.848554 GCAGCTTAGACCGTTGTTTTCAC 60.849 47.826 0.00 0.00 0.00 3.18
33 34 5.096849 GCTTAGACCGTTGTTTTCACAAAA 58.903 37.500 0.00 0.00 44.72 2.44
34 35 5.004061 GCTTAGACCGTTGTTTTCACAAAAC 59.996 40.000 5.13 5.13 44.72 2.43
62 63 3.738281 CGGTATAGTAAACTGCTGCTGCT 60.738 47.826 17.00 0.00 40.48 4.24
63 64 3.557595 GGTATAGTAAACTGCTGCTGCTG 59.442 47.826 18.66 18.66 42.70 4.41
93 101 2.352715 GGGCTTGTGGCTGTAAAATGTC 60.353 50.000 0.00 0.00 41.46 3.06
168 176 4.142038 GTGAAACCACCTATGAACAACCT 58.858 43.478 0.00 0.00 0.00 3.50
169 177 4.215613 GTGAAACCACCTATGAACAACCTC 59.784 45.833 0.00 0.00 0.00 3.85
204 213 2.202557 GCGGCCGGCAATTGTTAC 60.203 61.111 30.85 6.91 42.87 2.50
245 254 1.280421 GAGAGGATGAACCACCAGCTT 59.720 52.381 0.00 0.00 42.04 3.74
248 257 3.525199 AGAGGATGAACCACCAGCTTAAT 59.475 43.478 0.00 0.00 42.04 1.40
285 304 2.096481 TTGTGTCGGCTTTCGTTCGC 62.096 55.000 0.00 0.00 40.32 4.70
300 319 5.849357 TCGTTCGCTTCTTTTGCTAATTA 57.151 34.783 0.00 0.00 0.00 1.40
374 508 8.456032 GTGAAAATAGTTTACAAACGAAACGAC 58.544 33.333 0.00 0.00 43.51 4.34
402 536 2.767505 CGATAGTTAATCCACTGGCCC 58.232 52.381 0.00 0.00 0.00 5.80
435 569 0.666913 CCTACGTACGGATGGTCTGG 59.333 60.000 21.06 3.23 0.00 3.86
447 581 3.609853 GATGGTCTGGTTTGCAGTATCA 58.390 45.455 0.00 0.00 0.00 2.15
448 582 3.719268 TGGTCTGGTTTGCAGTATCAT 57.281 42.857 0.00 0.00 0.00 2.45
496 630 4.346734 CGCATAGCAACACTCATCTTTT 57.653 40.909 0.00 0.00 0.00 2.27
497 631 4.093514 CGCATAGCAACACTCATCTTTTG 58.906 43.478 0.00 0.00 0.00 2.44
498 632 4.378770 CGCATAGCAACACTCATCTTTTGT 60.379 41.667 0.00 0.00 0.00 2.83
499 633 5.091431 GCATAGCAACACTCATCTTTTGTC 58.909 41.667 0.00 0.00 0.00 3.18
500 634 5.106396 GCATAGCAACACTCATCTTTTGTCT 60.106 40.000 0.00 0.00 0.00 3.41
501 635 6.541086 CATAGCAACACTCATCTTTTGTCTC 58.459 40.000 0.00 0.00 0.00 3.36
502 636 4.454678 AGCAACACTCATCTTTTGTCTCA 58.545 39.130 0.00 0.00 0.00 3.27
503 637 4.514441 AGCAACACTCATCTTTTGTCTCAG 59.486 41.667 0.00 0.00 0.00 3.35
506 640 6.678900 GCAACACTCATCTTTTGTCTCAGTTT 60.679 38.462 0.00 0.00 0.00 2.66
507 641 7.467267 GCAACACTCATCTTTTGTCTCAGTTTA 60.467 37.037 0.00 0.00 0.00 2.01
508 642 8.562892 CAACACTCATCTTTTGTCTCAGTTTAT 58.437 33.333 0.00 0.00 0.00 1.40
509 643 9.778741 AACACTCATCTTTTGTCTCAGTTTATA 57.221 29.630 0.00 0.00 0.00 0.98
510 644 9.429359 ACACTCATCTTTTGTCTCAGTTTATAG 57.571 33.333 0.00 0.00 0.00 1.31
511 645 9.429359 CACTCATCTTTTGTCTCAGTTTATAGT 57.571 33.333 0.00 0.00 0.00 2.12
513 647 8.777865 TCATCTTTTGTCTCAGTTTATAGTGG 57.222 34.615 0.00 0.00 0.00 4.00
514 648 7.824289 TCATCTTTTGTCTCAGTTTATAGTGGG 59.176 37.037 0.00 0.00 0.00 4.61
515 649 6.472887 TCTTTTGTCTCAGTTTATAGTGGGG 58.527 40.000 0.00 0.00 0.00 4.96
519 653 6.442541 TGTCTCAGTTTATAGTGGGGAAAA 57.557 37.500 0.00 0.00 0.00 2.29
547 681 1.474330 CACCCTAATCAAACCCTGCC 58.526 55.000 0.00 0.00 0.00 4.85
627 1154 9.219603 TCTGTTTGTTTGATCAACTATAGGAAG 57.780 33.333 7.89 0.29 36.21 3.46
819 1350 2.279517 GCACTCGGTCTATGGGCG 60.280 66.667 0.00 0.00 0.00 6.13
820 1351 2.782222 GCACTCGGTCTATGGGCGA 61.782 63.158 0.00 0.00 0.00 5.54
823 1354 1.102222 ACTCGGTCTATGGGCGAGAC 61.102 60.000 0.00 4.70 42.24 3.36
846 1377 0.902984 ATCACCACCGTCCACTGCTA 60.903 55.000 0.00 0.00 0.00 3.49
873 1404 2.476051 CGCATCAACGGCAGACAC 59.524 61.111 0.00 0.00 0.00 3.67
940 1486 0.998928 ATTCCTATGTGGTGGGTGCA 59.001 50.000 0.00 0.00 37.07 4.57
1129 1681 1.595058 TTCTCCTCCTCCTCCTCCCC 61.595 65.000 0.00 0.00 0.00 4.81
1130 1682 3.036959 TCCTCCTCCTCCTCCCCC 61.037 72.222 0.00 0.00 0.00 5.40
1151 1703 2.124320 CCCGAAATCCGCACCCAT 60.124 61.111 0.00 0.00 36.84 4.00
1170 1722 4.238514 CCATATTCCGAAATCGAGAGGTC 58.761 47.826 4.04 0.00 43.02 3.85
1206 1759 4.168922 GAACGAAATTCCCCGATTGTTT 57.831 40.909 0.00 0.00 0.00 2.83
1208 1761 2.888414 ACGAAATTCCCCGATTGTTTGT 59.112 40.909 0.00 0.00 0.00 2.83
1223 1776 3.620300 TTGTCTCGTACGCGCCTGG 62.620 63.158 11.24 0.00 38.14 4.45
1230 1784 1.138047 CGTACGCGCCTGGAAGTAAG 61.138 60.000 5.73 0.00 0.00 2.34
1234 1788 1.696832 CGCGCCTGGAAGTAAGAAGC 61.697 60.000 0.00 0.00 0.00 3.86
1235 1789 0.391793 GCGCCTGGAAGTAAGAAGCT 60.392 55.000 0.00 0.00 0.00 3.74
1237 1791 2.427506 CGCCTGGAAGTAAGAAGCTTT 58.572 47.619 0.00 0.00 0.00 3.51
1238 1792 2.814336 CGCCTGGAAGTAAGAAGCTTTT 59.186 45.455 0.00 0.00 0.00 2.27
1258 1831 2.358322 TTTCCCCTATCCAATTCGCC 57.642 50.000 0.00 0.00 0.00 5.54
1266 1839 1.762708 ATCCAATTCGCCAATTCGGT 58.237 45.000 5.61 0.00 36.97 4.69
1270 1843 1.984990 CAATTCGCCAATTCGGTGTTG 59.015 47.619 7.17 3.39 46.24 3.33
1467 2051 8.943594 TTTTAGGGATATTGTTGTTGGTTAGT 57.056 30.769 0.00 0.00 0.00 2.24
1468 2052 8.570068 TTTAGGGATATTGTTGTTGGTTAGTC 57.430 34.615 0.00 0.00 0.00 2.59
1470 2054 7.504926 AGGGATATTGTTGTTGGTTAGTCTA 57.495 36.000 0.00 0.00 0.00 2.59
1479 2063 9.616156 TTGTTGTTGGTTAGTCTATTTACTTCA 57.384 29.630 0.00 0.00 0.00 3.02
1480 2064 9.268268 TGTTGTTGGTTAGTCTATTTACTTCAG 57.732 33.333 0.00 0.00 0.00 3.02
1481 2065 9.485206 GTTGTTGGTTAGTCTATTTACTTCAGA 57.515 33.333 0.00 0.00 0.00 3.27
1528 2112 4.030913 TCCTAGGATTCGATGTTTCTGGT 58.969 43.478 7.62 0.00 0.00 4.00
1606 2200 8.999431 TGGATTAAATAGGCTCGTATTTTGATC 58.001 33.333 11.31 13.20 34.93 2.92
1637 2231 6.758886 GCTCCTCGAATAGTTATATGGATTGG 59.241 42.308 0.00 0.00 0.00 3.16
1651 2245 1.406903 GATTGGAGGATTTGGGGCTG 58.593 55.000 0.00 0.00 0.00 4.85
1677 2271 6.012658 TGGAGCATGTTCTTCATTTAACAC 57.987 37.500 9.57 0.00 38.35 3.32
1763 2357 5.942872 AGTCTGTTCTGTTTTCAGTTGTTG 58.057 37.500 0.00 0.00 46.98 3.33
1764 2358 5.473504 AGTCTGTTCTGTTTTCAGTTGTTGT 59.526 36.000 0.00 0.00 46.98 3.32
1765 2359 6.016276 AGTCTGTTCTGTTTTCAGTTGTTGTT 60.016 34.615 0.00 0.00 46.98 2.83
1766 2360 7.174253 AGTCTGTTCTGTTTTCAGTTGTTGTTA 59.826 33.333 0.00 0.00 46.98 2.41
1783 2377 6.676950 TGTTGTTATTTACTTGGCATCACTG 58.323 36.000 0.00 0.00 0.00 3.66
1786 2380 7.701539 TGTTATTTACTTGGCATCACTGAAT 57.298 32.000 0.00 0.00 0.00 2.57
1851 2445 2.351726 GCTTACCTAATGCGTGAAGGTG 59.648 50.000 19.04 8.06 43.47 4.00
2076 2689 0.039708 GTGCAAGGTTCTTGCTGCTC 60.040 55.000 26.22 14.17 45.13 4.26
2078 2691 1.510480 GCAAGGTTCTTGCTGCTCGT 61.510 55.000 21.17 0.00 41.87 4.18
2090 2703 1.866063 GCTGCTCGTACTCTGTATGGC 60.866 57.143 0.00 0.00 0.00 4.40
2091 2704 1.405463 CTGCTCGTACTCTGTATGGCA 59.595 52.381 0.00 0.00 0.00 4.92
2130 2743 1.676006 ACTGTCCCTTTTTGCAAGTCG 59.324 47.619 0.00 0.00 0.00 4.18
2492 3121 6.324561 AGGAGAAGCAAAAAGAAGAATGAC 57.675 37.500 0.00 0.00 0.00 3.06
2654 3283 6.373005 TGATTTCAGGGTCTTAATCTGACA 57.627 37.500 0.00 0.00 37.28 3.58
2662 3291 8.004801 TCAGGGTCTTAATCTGACAGTATGATA 58.995 37.037 1.59 0.00 41.26 2.15
2698 3327 0.774491 AGCCCCACCTTAGGAAACCA 60.774 55.000 4.77 0.00 0.00 3.67
2715 3344 6.269769 AGGAAACCATGTACCAATGTCAATTT 59.730 34.615 0.00 0.00 0.00 1.82
2945 3578 5.992217 AGAGGTAAAGCAGAAACTTGTACAG 59.008 40.000 0.00 0.00 0.00 2.74
3490 4123 5.105146 GGTAGGTGATCCTATGATGGATGTC 60.105 48.000 0.31 0.00 46.00 3.06
3511 4144 2.607771 CGGGCCACAAATTTCAGTTCTG 60.608 50.000 4.39 0.00 0.00 3.02
3775 4411 8.272866 TGCATAATTGTTAATCGATTCAGTACG 58.727 33.333 15.25 0.00 32.85 3.67
3890 4526 8.242053 CAGAATCTTTAATCTTGTCTGTGCATT 58.758 33.333 0.00 0.00 0.00 3.56
4088 4736 1.473677 TCATGCACACTGCTATTTGCC 59.526 47.619 0.00 0.00 45.31 4.52
4092 4740 0.960364 CACACTGCTATTTGCCGGGT 60.960 55.000 2.18 0.00 43.32 5.28
4124 4772 6.207221 TGTTTGCTAATGTGACACATCTTCAT 59.793 34.615 21.05 8.12 37.97 2.57
4149 4797 1.225704 CCAGAGGGTCCTGAATGGC 59.774 63.158 0.00 0.00 36.29 4.40
4207 4855 2.294979 GCACTGATGGCAAGATCATCA 58.705 47.619 0.00 6.59 45.86 3.07
4266 4914 3.446442 AGCTTGGTTGGACATGAAGAT 57.554 42.857 0.00 0.00 0.00 2.40
4385 5039 7.345653 TGAAGTGGAAGATGTTACATCTCCTAT 59.654 37.037 25.61 12.06 0.00 2.57
4410 5064 4.261801 CACCAAAGACCCTCATAACGAAT 58.738 43.478 0.00 0.00 0.00 3.34
4445 5099 3.529533 CTGTTCATGAGGAGGCAAGTAG 58.470 50.000 0.00 0.00 0.00 2.57
4609 5265 8.686334 ACCAAAGTATGATTATGCTTTTACCAG 58.314 33.333 10.25 1.00 43.74 4.00
4777 5470 4.439837 GGAAGCAAGAGAAAGAATGATGCC 60.440 45.833 0.00 0.00 32.95 4.40
4792 5485 4.412796 TGATGCCTATCTGAAGTTCTGG 57.587 45.455 9.59 0.74 34.31 3.86
4828 5521 6.332976 AGTGACCCATATGATTTCCTCTTT 57.667 37.500 3.65 0.00 0.00 2.52
4962 5657 6.293081 CCAAGCAACTAGAATGATTATGTCCG 60.293 42.308 0.00 0.00 0.00 4.79
4992 5687 1.309950 CAGATTCAGCAGATGCCTGG 58.690 55.000 0.14 0.00 43.38 4.45
5187 5885 1.457303 GCTGTCGTGTGTTCAGTCATC 59.543 52.381 0.00 0.00 0.00 2.92
5188 5886 2.742774 CTGTCGTGTGTTCAGTCATCA 58.257 47.619 0.00 0.00 0.00 3.07
5189 5887 3.320626 CTGTCGTGTGTTCAGTCATCAT 58.679 45.455 0.00 0.00 0.00 2.45
5208 5906 6.596888 TCATCATTCAGAAGTAGCCAGAAAAG 59.403 38.462 0.00 0.00 0.00 2.27
5255 5953 2.627699 GTTTTCCAAAGCCAGGTGATGA 59.372 45.455 0.00 0.00 0.00 2.92
5328 6026 2.892215 TGAATTGCTGGACATTTGCTGA 59.108 40.909 0.00 0.00 0.00 4.26
5379 6077 4.820775 AGGATAAGGCCATCTAACAGAGA 58.179 43.478 5.01 0.00 39.01 3.10
5380 6078 4.591072 AGGATAAGGCCATCTAACAGAGAC 59.409 45.833 5.01 0.00 36.87 3.36
5381 6079 4.262678 GGATAAGGCCATCTAACAGAGACC 60.263 50.000 5.01 0.00 36.87 3.85
5382 6080 1.115467 AGGCCATCTAACAGAGACCG 58.885 55.000 5.01 0.00 36.87 4.79
5383 6081 0.824759 GGCCATCTAACAGAGACCGT 59.175 55.000 0.00 0.00 36.87 4.83
5465 6178 7.094890 ACTGAAACTGATCAAATGCTTCTACTG 60.095 37.037 0.00 0.00 0.00 2.74
5527 6306 2.599216 CAAAGGCCCTTGCATCCAT 58.401 52.632 0.00 0.00 40.13 3.41
5536 6315 3.871463 GCCCTTGCATCCATATACTCCAG 60.871 52.174 0.00 0.00 37.47 3.86
5613 6392 3.305720 CCCCATGGCTACTACTTAGTGA 58.694 50.000 6.09 0.00 37.10 3.41
5624 6403 8.039538 GGCTACTACTTAGTGACACCTTTATTT 58.960 37.037 0.84 0.00 37.10 1.40
5629 6408 6.296026 ACTTAGTGACACCTTTATTTCTGCA 58.704 36.000 0.84 0.00 0.00 4.41
5630 6409 6.770785 ACTTAGTGACACCTTTATTTCTGCAA 59.229 34.615 0.84 0.00 0.00 4.08
5788 6567 0.820871 CCAGAGCTAGTCCAGTGTCC 59.179 60.000 0.00 0.00 0.00 4.02
5810 6589 6.987404 GTCCTCTTCCTCAGGTATTTTATGTC 59.013 42.308 0.00 0.00 32.20 3.06
5812 6591 5.914033 TCTTCCTCAGGTATTTTATGTCGG 58.086 41.667 0.00 0.00 0.00 4.79
5833 6612 5.464389 TCGGTGCTTTACTTTTTACTCTCAC 59.536 40.000 0.00 0.00 0.00 3.51
5950 6732 4.883021 ATGGAGTCCAAGAGGTAGTCTA 57.117 45.455 17.71 0.00 36.95 2.59
5951 6733 4.883021 TGGAGTCCAAGAGGTAGTCTAT 57.117 45.455 10.20 0.00 32.65 1.98
5985 6767 8.612619 CCTATGCACTGGTATACTTTTAAGTTG 58.387 37.037 2.25 0.00 40.37 3.16
6073 6855 3.694566 CCACCATAACCCTTTGAGCTAAC 59.305 47.826 0.00 0.00 0.00 2.34
6275 7062 1.338769 CGAAGGAATTCGGACCTTGGT 60.339 52.381 0.00 0.00 45.08 3.67
6630 7417 7.974504 ACTTGATTTCTACAAAGAAGGTAGGA 58.025 34.615 0.00 0.00 42.60 2.94
6633 7420 9.807921 TTGATTTCTACAAAGAAGGTAGGATTT 57.192 29.630 0.00 0.00 42.60 2.17
6634 7421 9.449719 TGATTTCTACAAAGAAGGTAGGATTTC 57.550 33.333 0.00 0.00 42.60 2.17
6968 7756 3.273919 ACGCATTGCAGAAGAAGAAAC 57.726 42.857 9.69 0.00 0.00 2.78
7054 7845 5.650266 TGGTGCGTAAATACTGGAATTGATT 59.350 36.000 0.00 0.00 0.00 2.57
7160 7951 3.806949 TGTGTATGGGAAAAGAAGGCT 57.193 42.857 0.00 0.00 0.00 4.58
7161 7952 4.919774 TGTGTATGGGAAAAGAAGGCTA 57.080 40.909 0.00 0.00 0.00 3.93
7232 8025 6.070995 GGATCCTGAAATCACCACGGTATATA 60.071 42.308 3.84 0.00 0.00 0.86
7233 8026 6.928348 TCCTGAAATCACCACGGTATATAT 57.072 37.500 0.00 0.00 0.00 0.86
7337 8130 7.926018 TGTAGCATGGTCAGTTTGTATAGTATG 59.074 37.037 0.00 0.00 0.00 2.39
7382 8177 2.108250 ACCTTGTGCTAGGGTTTGTGAT 59.892 45.455 4.84 0.00 34.61 3.06
7417 8214 6.325919 TGTCGCATCTTTTTAATTTGACCT 57.674 33.333 0.00 0.00 0.00 3.85
7472 8270 0.944311 GCTCGTTTCCTGAAGCACGA 60.944 55.000 6.63 6.63 39.27 4.35
7473 8271 1.714794 CTCGTTTCCTGAAGCACGAT 58.285 50.000 7.13 0.00 40.66 3.73
7477 8275 2.223144 CGTTTCCTGAAGCACGATTGAA 59.777 45.455 0.00 0.00 34.49 2.69
7516 8314 5.935789 AGATTCCGAATTAACGAAAAGGTGA 59.064 36.000 0.00 0.00 35.09 4.02
7520 8318 6.972722 TCCGAATTAACGAAAAGGTGAAAAT 58.027 32.000 0.00 0.00 35.09 1.82
7528 8326 7.764695 AACGAAAAGGTGAAAATTCGAAAAT 57.235 28.000 12.95 0.00 45.45 1.82
7531 8329 7.043656 ACGAAAAGGTGAAAATTCGAAAATGAC 60.044 33.333 12.95 0.00 45.45 3.06
7533 8331 6.405278 AAGGTGAAAATTCGAAAATGACCT 57.595 33.333 0.00 7.69 32.59 3.85
7536 8334 6.265422 AGGTGAAAATTCGAAAATGACCTTCT 59.735 34.615 0.00 0.00 0.00 2.85
7537 8335 6.363357 GGTGAAAATTCGAAAATGACCTTCTG 59.637 38.462 0.00 0.00 0.00 3.02
7622 8421 5.776744 CTGAAAAATAAAGTTGGCTGAGCT 58.223 37.500 3.72 0.00 0.00 4.09
7663 8476 4.855531 CCATGCGGCCTTATTAACTTTAC 58.144 43.478 0.00 0.00 0.00 2.01
7668 8481 4.274214 GCGGCCTTATTAACTTTACGGATT 59.726 41.667 0.00 0.00 0.00 3.01
7702 8515 7.675962 TTTTAGCGATTACACTGTTACCAAT 57.324 32.000 0.00 0.00 0.00 3.16
7708 8521 6.457663 GCGATTACACTGTTACCAATAATGCA 60.458 38.462 0.00 0.00 0.00 3.96
7728 8541 3.545078 GCAGTTCAGCTTCATAATTTGCG 59.455 43.478 0.00 0.00 0.00 4.85
7840 8653 3.119637 AGTGACACGACCAAAACCAAAAG 60.120 43.478 0.00 0.00 0.00 2.27
7940 8753 2.035321 TCAGTGTCATAACTCGTGTGCA 59.965 45.455 0.00 0.00 0.00 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 1.009829 CAACGGTCTAAGCTGCATCC 58.990 55.000 1.02 0.00 0.00 3.51
29 30 9.269415 GCAGTTTACTATACCGTTTATGTTTTG 57.731 33.333 0.00 0.00 0.00 2.44
33 34 6.257193 GCAGCAGTTTACTATACCGTTTATGT 59.743 38.462 0.00 0.00 0.00 2.29
34 35 6.479001 AGCAGCAGTTTACTATACCGTTTATG 59.521 38.462 0.00 0.00 0.00 1.90
62 63 2.041081 AGCCACAAGCCCTGTTAATACA 59.959 45.455 0.00 0.00 45.47 2.29
63 64 2.423538 CAGCCACAAGCCCTGTTAATAC 59.576 50.000 0.00 0.00 45.47 1.89
65 66 1.203050 ACAGCCACAAGCCCTGTTAAT 60.203 47.619 0.00 0.00 45.47 1.40
93 101 2.036733 TCTAAACGGAACACAGTCTGGG 59.963 50.000 0.00 0.00 0.00 4.45
168 176 1.254026 CTCGTAGACACTTGGGTGGA 58.746 55.000 1.29 0.00 46.85 4.02
169 177 0.389948 GCTCGTAGACACTTGGGTGG 60.390 60.000 1.29 0.00 46.85 4.61
204 213 0.461870 TCGAGCCCAACGAATGATGG 60.462 55.000 0.00 0.00 37.76 3.51
248 257 8.714179 CCGACACAATCTGTTACTTTATGTTAA 58.286 33.333 0.00 0.00 31.03 2.01
357 491 3.949588 CGTGAGTCGTTTCGTTTGTAAAC 59.050 43.478 0.00 0.00 34.25 2.01
374 508 3.486108 GTGGATTAACTATCGTGCGTGAG 59.514 47.826 0.00 0.00 33.82 3.51
402 536 1.544691 ACGTAGGACTAGGTGCAACAG 59.455 52.381 3.64 1.64 39.98 3.16
484 618 9.429359 CTATAAACTGAGACAAAAGATGAGTGT 57.571 33.333 0.00 0.00 0.00 3.55
496 630 6.442541 TTTTCCCCACTATAAACTGAGACA 57.557 37.500 0.00 0.00 0.00 3.41
519 653 2.990740 TGATTAGGGTGGTTGCCTTT 57.009 45.000 0.00 0.00 0.00 3.11
523 657 1.548719 GGGTTTGATTAGGGTGGTTGC 59.451 52.381 0.00 0.00 0.00 4.17
531 665 4.713792 ATCTAGGCAGGGTTTGATTAGG 57.286 45.455 0.00 0.00 0.00 2.69
621 1148 6.438186 TGATGATGATACATTGCCTTCCTA 57.562 37.500 0.00 0.00 0.00 2.94
819 1350 2.240162 GACGGTGGTGATGGGGTCTC 62.240 65.000 0.00 0.00 0.00 3.36
820 1351 2.203938 ACGGTGGTGATGGGGTCT 60.204 61.111 0.00 0.00 0.00 3.85
823 1354 3.326578 TGGACGGTGGTGATGGGG 61.327 66.667 0.00 0.00 0.00 4.96
1151 1703 4.994907 TTGACCTCTCGATTTCGGAATA 57.005 40.909 0.00 0.00 40.29 1.75
1170 1722 1.800681 GTTCCCGGCGGAGATTTTG 59.199 57.895 30.79 8.87 40.10 2.44
1206 1759 4.111016 CCAGGCGCGTACGAGACA 62.111 66.667 26.83 0.00 43.93 3.41
1208 1761 3.047718 CTTCCAGGCGCGTACGAGA 62.048 63.158 23.53 3.99 43.93 4.04
1237 1791 3.028130 GGCGAATTGGATAGGGGAAAAA 58.972 45.455 0.00 0.00 0.00 1.94
1238 1792 2.024846 TGGCGAATTGGATAGGGGAAAA 60.025 45.455 0.00 0.00 0.00 2.29
1241 1795 1.217916 TTGGCGAATTGGATAGGGGA 58.782 50.000 0.00 0.00 0.00 4.81
1242 1796 2.292828 ATTGGCGAATTGGATAGGGG 57.707 50.000 0.00 0.00 0.00 4.79
1244 1798 2.226437 CCGAATTGGCGAATTGGATAGG 59.774 50.000 15.91 6.38 31.58 2.57
1245 1799 2.878406 ACCGAATTGGCGAATTGGATAG 59.122 45.455 20.89 8.61 43.94 2.08
1247 1801 1.405105 CACCGAATTGGCGAATTGGAT 59.595 47.619 20.89 3.95 43.94 3.41
1258 1831 0.110238 CACGCTCCAACACCGAATTG 60.110 55.000 0.00 0.00 0.00 2.32
1447 2028 8.747538 AATAGACTAACCAACAACAATATCCC 57.252 34.615 0.00 0.00 0.00 3.85
1470 2054 8.924511 TCCAAGTTCTGAATTCTGAAGTAAAT 57.075 30.769 26.41 14.40 36.75 1.40
1479 2063 4.104738 TGGTTCCTCCAAGTTCTGAATTCT 59.895 41.667 7.05 0.00 44.12 2.40
1480 2064 4.398319 TGGTTCCTCCAAGTTCTGAATTC 58.602 43.478 0.00 0.00 44.12 2.17
1481 2065 4.453480 TGGTTCCTCCAAGTTCTGAATT 57.547 40.909 0.00 0.00 44.12 2.17
1513 2097 4.508662 GAGAGGAACCAGAAACATCGAAT 58.491 43.478 0.00 0.00 0.00 3.34
1514 2098 3.614150 CGAGAGGAACCAGAAACATCGAA 60.614 47.826 0.00 0.00 0.00 3.71
1517 2101 2.003301 GCGAGAGGAACCAGAAACATC 58.997 52.381 0.00 0.00 0.00 3.06
1519 2103 1.000955 GAGCGAGAGGAACCAGAAACA 59.999 52.381 0.00 0.00 0.00 2.83
1528 2112 1.633774 ACAGGAAAGAGCGAGAGGAA 58.366 50.000 0.00 0.00 0.00 3.36
1606 2200 1.858091 ACTATTCGAGGAGCGCAATG 58.142 50.000 11.47 0.00 40.61 2.82
1637 2231 1.755783 CAGGCAGCCCCAAATCCTC 60.756 63.158 8.22 0.00 35.39 3.71
1651 2245 1.760192 ATGAAGAACATGCTCCAGGC 58.240 50.000 0.00 0.00 37.87 4.85
1677 2271 8.798402 TGGGTATTTTTACATGTGGACTTTTAG 58.202 33.333 9.11 0.00 0.00 1.85
1763 2357 7.761409 TCATTCAGTGATGCCAAGTAAATAAC 58.239 34.615 0.00 0.00 0.00 1.89
1764 2358 7.936496 TCATTCAGTGATGCCAAGTAAATAA 57.064 32.000 0.00 0.00 0.00 1.40
1881 2476 2.851263 TTAACCTTCACGCACTGGAT 57.149 45.000 0.00 0.00 0.00 3.41
1882 2477 2.851263 ATTAACCTTCACGCACTGGA 57.149 45.000 0.00 0.00 0.00 3.86
1883 2478 2.936498 CCTATTAACCTTCACGCACTGG 59.064 50.000 0.00 0.00 0.00 4.00
1884 2479 3.596214 ACCTATTAACCTTCACGCACTG 58.404 45.455 0.00 0.00 0.00 3.66
1966 2564 9.296400 GTTTATACACGTGGCATCAATTAATTT 57.704 29.630 21.57 0.00 0.00 1.82
2046 2656 6.678900 GCAAGAACCTTGCACTGATTATTAGG 60.679 42.308 22.33 0.00 44.34 2.69
2076 2689 3.179830 GTTCAGTGCCATACAGAGTACG 58.820 50.000 0.00 0.00 0.00 3.67
2078 2691 4.882842 TTGTTCAGTGCCATACAGAGTA 57.117 40.909 0.00 0.00 0.00 2.59
2090 2703 4.730042 CAGTGTCGTCAATTTTGTTCAGTG 59.270 41.667 0.00 0.00 0.00 3.66
2091 2704 4.394920 ACAGTGTCGTCAATTTTGTTCAGT 59.605 37.500 0.00 0.00 0.00 3.41
2130 2743 2.698797 TGATTACAGGTGCTAGTAGGGC 59.301 50.000 0.00 0.00 0.00 5.19
2225 2852 5.615289 ACAAATTAGTGGGCTAGCTAGATG 58.385 41.667 25.15 0.00 0.00 2.90
2274 2901 7.759489 TCCATATTGTAGTCAAAGCAAAAGT 57.241 32.000 0.00 0.00 37.11 2.66
2520 3149 2.868583 CGGCCTGTAGATCTTGAACATG 59.131 50.000 0.00 0.00 0.00 3.21
2662 3291 6.071320 GTGGGGCTATTGGAAAGAAATCTAT 58.929 40.000 0.00 0.00 0.00 1.98
2698 3327 7.615365 ACACATAGGAAATTGACATTGGTACAT 59.385 33.333 0.00 0.00 39.30 2.29
2715 3344 1.208052 GCCTCTTGAGCACACATAGGA 59.792 52.381 9.04 0.00 0.00 2.94
3022 3655 5.245531 TCAGCGTAATCAAATTCCTGAGTT 58.754 37.500 0.00 0.00 0.00 3.01
3479 4112 1.149174 GTGGCCCGACATCCATCAT 59.851 57.895 0.00 0.00 34.47 2.45
3490 4123 1.613437 AGAACTGAAATTTGTGGCCCG 59.387 47.619 0.00 0.00 0.00 6.13
3733 4369 5.749596 TTATGCATCAAACCAATCCTACG 57.250 39.130 0.19 0.00 0.00 3.51
3853 4489 8.316497 AGATTAAAGATTCTGACCTCTCATCA 57.684 34.615 0.00 0.00 0.00 3.07
3890 4526 5.514500 AGGCATTAGTCTGGAAACCTTAA 57.486 39.130 0.00 0.00 0.00 1.85
3892 4528 4.388577 AAGGCATTAGTCTGGAAACCTT 57.611 40.909 0.00 0.00 0.00 3.50
4088 4736 1.588674 TAGCAAACACAAGACACCCG 58.411 50.000 0.00 0.00 0.00 5.28
4092 4740 4.637977 TGTCACATTAGCAAACACAAGACA 59.362 37.500 0.00 0.00 0.00 3.41
4149 4797 1.335597 TGTCTGTCGTAGTTTGCCTCG 60.336 52.381 0.00 0.00 0.00 4.63
4207 4855 0.179073 CGCTGTGGCCTAGCATAACT 60.179 55.000 25.36 0.00 41.18 2.24
4385 5039 3.153919 GTTATGAGGGTCTTTGGTGCAA 58.846 45.455 0.00 0.00 0.00 4.08
4410 5064 2.131854 TGAACAGGGGTCAAAGAAGGA 58.868 47.619 0.00 0.00 0.00 3.36
4445 5099 5.966636 TTGTACGCTCAACATGTGATATC 57.033 39.130 0.00 0.00 35.07 1.63
4677 5333 8.417106 TCTTAGATAGATGGTTAGACTTTGCTG 58.583 37.037 0.00 0.00 0.00 4.41
4748 5441 4.696479 TCTTTCTCTTGCTTCCTTCAGT 57.304 40.909 0.00 0.00 0.00 3.41
4765 5458 7.282675 CAGAACTTCAGATAGGCATCATTCTTT 59.717 37.037 0.00 0.00 33.21 2.52
4777 5470 3.772025 ACTGGGTCCAGAACTTCAGATAG 59.228 47.826 22.46 0.00 46.30 2.08
4792 5485 0.321996 GGTCACTTCCAGACTGGGTC 59.678 60.000 21.56 3.19 38.32 4.46
4962 5657 1.403323 GCTGAATCTGCCCTTTGCTAC 59.597 52.381 0.27 0.00 42.00 3.58
4992 5687 5.756833 GGATTCAAGATCAAATTGGCAATCC 59.243 40.000 14.04 2.49 35.56 3.01
5172 5870 3.989817 TCTGAATGATGACTGAACACACG 59.010 43.478 0.00 0.00 0.00 4.49
5187 5885 7.856145 ATACTTTTCTGGCTACTTCTGAATG 57.144 36.000 0.00 0.00 0.00 2.67
5188 5886 8.870075 AAATACTTTTCTGGCTACTTCTGAAT 57.130 30.769 0.00 0.00 0.00 2.57
5189 5887 8.567948 CAAAATACTTTTCTGGCTACTTCTGAA 58.432 33.333 0.00 0.00 0.00 3.02
5255 5953 5.582953 TGGAGATTCCATTTCAATTCCTGT 58.417 37.500 0.00 0.00 42.67 4.00
5328 6026 6.097412 GGATGAGCCTGATTCTTGGTAATTTT 59.903 38.462 0.00 0.00 0.00 1.82
5379 6077 5.302360 TGTTAGTAGAAGCATTTGAACGGT 58.698 37.500 0.00 0.00 0.00 4.83
5380 6078 5.856126 TGTTAGTAGAAGCATTTGAACGG 57.144 39.130 0.00 0.00 0.00 4.44
5381 6079 6.797033 CCTTTGTTAGTAGAAGCATTTGAACG 59.203 38.462 0.00 0.00 0.00 3.95
5382 6080 6.582672 GCCTTTGTTAGTAGAAGCATTTGAAC 59.417 38.462 0.00 0.00 0.00 3.18
5383 6081 6.264292 TGCCTTTGTTAGTAGAAGCATTTGAA 59.736 34.615 0.00 0.00 0.00 2.69
5465 6178 8.552083 AAAGAATAATTCCATTTGCCTTTGTC 57.448 30.769 0.00 0.00 0.00 3.18
5562 6341 5.784906 TCCATGGTTGTCTGGATAGCATATA 59.215 40.000 12.58 0.00 36.63 0.86
5613 6392 8.367156 ACATGTATTTTGCAGAAATAAAGGTGT 58.633 29.630 15.05 10.25 27.20 4.16
5624 6403 7.230510 ACCTGTTAGAAACATGTATTTTGCAGA 59.769 33.333 0.00 0.00 41.26 4.26
5629 6408 9.582648 AGGTTACCTGTTAGAAACATGTATTTT 57.417 29.630 1.74 0.00 40.51 1.82
5630 6409 9.227777 GAGGTTACCTGTTAGAAACATGTATTT 57.772 33.333 9.39 0.00 40.51 1.40
5788 6567 5.986135 CCGACATAAAATACCTGAGGAAGAG 59.014 44.000 4.99 0.00 0.00 2.85
5810 6589 5.611844 CGTGAGAGTAAAAAGTAAAGCACCG 60.612 44.000 0.00 0.00 0.00 4.94
5812 6591 5.464389 TCCGTGAGAGTAAAAAGTAAAGCAC 59.536 40.000 0.00 0.00 0.00 4.40
5833 6612 1.001378 CAACTTGACAAGGGCTTTCCG 60.001 52.381 19.16 0.00 41.52 4.30
5924 6704 5.342866 ACTACCTCTTGGACTCCATAACTT 58.657 41.667 0.00 0.00 37.04 2.66
5931 6711 4.339814 CACATAGACTACCTCTTGGACTCC 59.660 50.000 0.00 0.00 37.04 3.85
6275 7062 0.950555 GACTGTCAGCCATGCGACAA 60.951 55.000 2.24 0.00 39.75 3.18
6751 7538 0.962489 CGTAGAGGGCCTGTAGATGG 59.038 60.000 12.95 0.00 0.00 3.51
6968 7756 3.023119 TCTAAGCTCCTCAGAAGCAGAG 58.977 50.000 0.00 0.00 0.00 3.35
7054 7845 2.511373 GCATGATCGTGGCGACCA 60.511 61.111 16.59 0.00 39.18 4.02
7161 7952 7.607991 GCCCAATATACAAACAGATATACAGCT 59.392 37.037 0.00 0.00 0.00 4.24
7232 8025 3.126001 ACGACAACTCCAACACATCAT 57.874 42.857 0.00 0.00 0.00 2.45
7233 8026 2.611751 CAACGACAACTCCAACACATCA 59.388 45.455 0.00 0.00 0.00 3.07
7337 8130 6.907212 GTCACAATCGGTTCATTCAATGATAC 59.093 38.462 0.00 2.90 39.39 2.24
7346 8141 3.253188 CACAAGGTCACAATCGGTTCATT 59.747 43.478 0.00 0.00 0.00 2.57
7412 8209 2.126057 TCCATCACCATGCATAGGTCA 58.874 47.619 15.32 6.17 37.23 4.02
7417 8214 6.541934 TTCAAATTTCCATCACCATGCATA 57.458 33.333 0.00 0.00 0.00 3.14
7477 8275 3.317993 CGGAATCTGGGTTTTTGAACACT 59.682 43.478 0.00 0.00 0.00 3.55
7516 8314 8.579863 AGAATCAGAAGGTCATTTTCGAATTTT 58.420 29.630 0.00 0.00 0.00 1.82
7520 8318 6.230472 TGAGAATCAGAAGGTCATTTTCGAA 58.770 36.000 0.00 0.00 42.56 3.71
7593 8392 5.049828 GCCAACTTTATTTTTCAGCTGTGT 58.950 37.500 14.67 0.00 0.00 3.72
7594 8393 5.176223 CAGCCAACTTTATTTTTCAGCTGTG 59.824 40.000 14.67 0.00 40.16 3.66
7597 8396 5.776744 CTCAGCCAACTTTATTTTTCAGCT 58.223 37.500 0.00 0.00 0.00 4.24
7663 8476 6.583912 TCGCTAAAATTCAGACTAAATCCG 57.416 37.500 0.00 0.00 0.00 4.18
7668 8481 8.869897 CAGTGTAATCGCTAAAATTCAGACTAA 58.130 33.333 0.00 0.00 32.72 2.24
7702 8515 6.753279 GCAAATTATGAAGCTGAACTGCATTA 59.247 34.615 6.47 0.00 42.63 1.90
7708 8521 3.191162 TGCGCAAATTATGAAGCTGAACT 59.809 39.130 8.16 0.00 35.89 3.01
7728 8541 5.512434 CCAAAAGTGTCAAAATTTTGCTTGC 59.488 36.000 23.36 14.16 40.77 4.01
7840 8653 2.877786 CCCAAGCCAAATCAACCAAAAC 59.122 45.455 0.00 0.00 0.00 2.43
7843 8656 0.396060 GCCCAAGCCAAATCAACCAA 59.604 50.000 0.00 0.00 0.00 3.67
7923 8736 2.296190 AGTCTGCACACGAGTTATGACA 59.704 45.455 0.00 0.00 0.00 3.58
7924 8737 2.947852 AGTCTGCACACGAGTTATGAC 58.052 47.619 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.