Multiple sequence alignment - TraesCS7D01G375300

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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 TraesCS7D01G375300 chr7D 100.000 4384 0 0 1 4384 485539677 485544060 0.000000e+00 8096.0
1 TraesCS7D01G375300 chr7A 93.669 2685 111 26 1692 4361 553996345 553998985 0.000000e+00 3962.0
2 TraesCS7D01G375300 chr7A 95.262 401 13 4 747 1143 553995293 553995691 8.000000e-177 630.0
3 TraesCS7D01G375300 chr7A 92.806 417 27 3 1271 1684 553995879 553996295 6.270000e-168 601.0
4 TraesCS7D01G375300 chr7A 81.421 183 28 4 3689 3869 523193367 523193189 1.270000e-30 145.0
5 TraesCS7D01G375300 chr7B 95.640 2179 71 9 1692 3863 513304700 513306861 0.000000e+00 3476.0
6 TraesCS7D01G375300 chr7B 91.144 734 63 2 1 732 308844584 308843851 0.000000e+00 994.0
7 TraesCS7D01G375300 chr7B 93.917 411 18 5 746 1155 513303594 513303998 8.060000e-172 614.0
8 TraesCS7D01G375300 chr7B 86.441 472 42 7 1216 1684 513304198 513304650 8.470000e-137 497.0
9 TraesCS7D01G375300 chr7B 93.750 48 3 0 3633 3680 513306491 513306538 6.080000e-09 73.1
10 TraesCS7D01G375300 chr4D 94.595 703 38 0 1 703 353429522 353428820 0.000000e+00 1088.0
11 TraesCS7D01G375300 chr4D 91.405 733 60 3 2 732 105925710 105926441 0.000000e+00 1002.0
12 TraesCS7D01G375300 chr4D 87.500 80 9 1 1456 1534 442176703 442176624 1.680000e-14 91.6
13 TraesCS7D01G375300 chr1A 92.308 741 55 2 1 739 250032127 250031387 0.000000e+00 1051.0
14 TraesCS7D01G375300 chr1A 80.508 118 15 5 1904 2017 427812942 427812829 2.810000e-12 84.2
15 TraesCS7D01G375300 chr5B 92.795 694 50 0 1 694 145841594 145840901 0.000000e+00 1005.0
16 TraesCS7D01G375300 chr5B 90.574 732 65 4 2 731 206079468 206080197 0.000000e+00 966.0
17 TraesCS7D01G375300 chr5B 90.450 733 67 3 2 732 372565809 372565078 0.000000e+00 963.0
18 TraesCS7D01G375300 chr5B 83.704 135 16 5 3685 3818 697498035 697498164 5.950000e-24 122.0
19 TraesCS7D01G375300 chr4B 91.293 735 61 3 1 732 151911091 151911825 0.000000e+00 1000.0
20 TraesCS7D01G375300 chr4B 85.000 80 11 1 1456 1534 549144031 549143952 3.630000e-11 80.5
21 TraesCS7D01G375300 chr4B 92.308 39 1 2 3765 3802 584848680 584848643 2.000000e-03 54.7
22 TraesCS7D01G375300 chr4B 92.308 39 1 2 3765 3802 584873968 584873931 2.000000e-03 54.7
23 TraesCS7D01G375300 chr4B 92.308 39 1 2 3765 3802 584899348 584899311 2.000000e-03 54.7
24 TraesCS7D01G375300 chrUn 91.156 735 62 3 1 732 407864453 407865187 0.000000e+00 994.0
25 TraesCS7D01G375300 chr6D 88.391 491 48 8 3892 4377 329882418 329881932 2.270000e-162 582.0
26 TraesCS7D01G375300 chr6D 87.149 498 56 8 3892 4384 229297120 229296626 3.830000e-155 558.0
27 TraesCS7D01G375300 chr6A 87.324 497 56 6 3892 4383 439305522 439306016 2.960000e-156 562.0
28 TraesCS7D01G375300 chr6B 87.349 498 52 9 3892 4382 649816294 649815801 1.060000e-155 560.0
29 TraesCS7D01G375300 chr6B 87.123 497 56 7 3892 4383 490633676 490634169 1.380000e-154 556.0
30 TraesCS7D01G375300 chr3D 87.129 505 51 14 3887 4383 65401352 65401850 1.060000e-155 560.0
31 TraesCS7D01G375300 chr3D 87.123 497 57 6 3892 4383 356639678 356639184 1.380000e-154 556.0
32 TraesCS7D01G375300 chr3D 87.123 497 55 8 3892 4383 381870240 381870732 4.950000e-154 555.0
33 TraesCS7D01G375300 chr4A 78.218 202 25 12 3683 3869 686929940 686930137 1.290000e-20 111.0
34 TraesCS7D01G375300 chr1B 80.833 120 13 7 1904 2018 445428542 445428428 7.810000e-13 86.1
35 TraesCS7D01G375300 chr1B 77.027 148 29 4 3685 3827 599246229 599246376 3.630000e-11 80.5
36 TraesCS7D01G375300 chr1D 79.832 119 16 5 1904 2018 330544305 330544191 3.630000e-11 80.5


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 TraesCS7D01G375300 chr7D 485539677 485544060 4383 False 8096.000 8096 100.000000 1 4384 1 chr7D.!!$F1 4383
1 TraesCS7D01G375300 chr7A 553995293 553998985 3692 False 1731.000 3962 93.912333 747 4361 3 chr7A.!!$F1 3614
2 TraesCS7D01G375300 chr7B 513303594 513306861 3267 False 1165.025 3476 92.437000 746 3863 4 chr7B.!!$F1 3117
3 TraesCS7D01G375300 chr7B 308843851 308844584 733 True 994.000 994 91.144000 1 732 1 chr7B.!!$R1 731
4 TraesCS7D01G375300 chr4D 353428820 353429522 702 True 1088.000 1088 94.595000 1 703 1 chr4D.!!$R1 702
5 TraesCS7D01G375300 chr4D 105925710 105926441 731 False 1002.000 1002 91.405000 2 732 1 chr4D.!!$F1 730
6 TraesCS7D01G375300 chr1A 250031387 250032127 740 True 1051.000 1051 92.308000 1 739 1 chr1A.!!$R1 738
7 TraesCS7D01G375300 chr5B 145840901 145841594 693 True 1005.000 1005 92.795000 1 694 1 chr5B.!!$R1 693
8 TraesCS7D01G375300 chr5B 206079468 206080197 729 False 966.000 966 90.574000 2 731 1 chr5B.!!$F1 729
9 TraesCS7D01G375300 chr5B 372565078 372565809 731 True 963.000 963 90.450000 2 732 1 chr5B.!!$R2 730
10 TraesCS7D01G375300 chr4B 151911091 151911825 734 False 1000.000 1000 91.293000 1 732 1 chr4B.!!$F1 731
11 TraesCS7D01G375300 chrUn 407864453 407865187 734 False 994.000 994 91.156000 1 732 1 chrUn.!!$F1 731

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
570 571 0.107017 GCTAGGGCAGGAGCATTTGA 60.107 55.000 0.00 0.00 44.61 2.69 F
1286 1462 0.254178 GGGGCTCTGCTCATGAGAAA 59.746 55.000 27.04 12.26 33.68 2.52 F
1345 1521 1.347707 TGGAGTACAAGGTGAAGCTGG 59.652 52.381 0.00 0.00 0.00 4.85 F
2932 3153 0.666577 ACGCACGTACTTGCTCTTCC 60.667 55.000 20.55 0.00 40.62 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2343 2564 1.377333 GTCCCTGTACTTGGCCTGC 60.377 63.158 3.32 0.0 0.0 4.85 R
2932 3153 1.372087 GCCGGCATGGACAAGAAGAG 61.372 60.000 24.80 0.0 42.0 2.85 R
2981 3205 2.456577 TGATCACAGATCGAACTCCCA 58.543 47.619 0.00 0.0 0.0 4.37 R
3883 4128 0.761802 TGTGGGCTATCACACACACA 59.238 50.000 0.00 0.0 42.2 3.72 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
52 53 3.511934 GGAATGTGACTGGAGTCTACACT 59.488 47.826 8.24 1.66 44.99 3.55
61 62 3.165071 TGGAGTCTACACTGCATCTTCA 58.835 45.455 0.00 0.00 45.40 3.02
156 157 6.348132 CCACTTGCGTGTAAAATCTTCATGTA 60.348 38.462 0.00 0.00 39.55 2.29
197 198 1.340308 TGTGGACGTCGGATAGAAGGA 60.340 52.381 9.92 0.00 32.45 3.36
217 218 3.326747 GACTAGACACGGTTTGCAAGAT 58.673 45.455 0.00 0.00 0.00 2.40
258 259 4.437682 TTTGTGACCAAGAGGAAGACAT 57.562 40.909 0.00 0.00 38.69 3.06
286 287 3.888323 ACCACATCTTGCAACAATGTGTA 59.112 39.130 30.05 0.26 45.58 2.90
478 479 1.014564 GGAAACAGAGGAACGCGAGG 61.015 60.000 15.93 0.00 0.00 4.63
570 571 0.107017 GCTAGGGCAGGAGCATTTGA 60.107 55.000 0.00 0.00 44.61 2.69
622 624 3.635869 TAGGAGTGGGGTGGAGGCC 62.636 68.421 0.00 0.00 0.00 5.19
649 651 1.408266 GGGTCGGCTTGTGATTACCAT 60.408 52.381 0.00 0.00 0.00 3.55
709 712 7.344095 TCTTTCTATAAAGCTAAGGTACGCT 57.656 36.000 0.00 0.00 41.64 5.07
710 713 8.455903 TCTTTCTATAAAGCTAAGGTACGCTA 57.544 34.615 0.00 0.00 41.64 4.26
777 780 9.722184 AATGTAATCATCATCAGTTATCCTCTG 57.278 33.333 0.00 0.00 32.56 3.35
814 817 1.235724 GTTCTCCCAAACGAACCAGG 58.764 55.000 0.00 0.00 34.83 4.45
909 914 0.602638 TGGTTGCTGGTAGTTGCTCG 60.603 55.000 0.00 0.00 0.00 5.03
921 926 1.742880 TTGCTCGCTCCTGTCATGC 60.743 57.895 0.00 0.00 0.00 4.06
938 943 4.391830 GTCATGCGATTTCTACTTGGTTGA 59.608 41.667 0.00 0.00 0.00 3.18
939 944 5.065218 GTCATGCGATTTCTACTTGGTTGAT 59.935 40.000 0.00 0.00 0.00 2.57
940 945 6.257849 GTCATGCGATTTCTACTTGGTTGATA 59.742 38.462 0.00 0.00 0.00 2.15
997 1007 3.699038 CTCTCTCTGAACCTAACTCCCAG 59.301 52.174 0.00 0.00 0.00 4.45
1032 1042 2.422231 CGAGGAGAGGGTGGAGCTG 61.422 68.421 0.00 0.00 0.00 4.24
1101 1111 6.653645 GAGGATCATCTATGGCCGACCAAG 62.654 54.167 0.00 0.00 42.77 3.61
1170 1214 3.769536 CTGTTTGTGGGACAGTTTTCAC 58.230 45.455 0.00 0.00 41.80 3.18
1252 1428 2.626088 GCTCTGCGCAAATTCTCTTT 57.374 45.000 13.05 0.00 38.92 2.52
1269 1445 6.978343 TCTCTTTTTATGACATGTAACGGG 57.022 37.500 0.00 0.00 0.00 5.28
1286 1462 0.254178 GGGGCTCTGCTCATGAGAAA 59.746 55.000 27.04 12.26 33.68 2.52
1296 1472 4.005650 TGCTCATGAGAAATCACCTTGTC 58.994 43.478 27.04 4.14 0.00 3.18
1345 1521 1.347707 TGGAGTACAAGGTGAAGCTGG 59.652 52.381 0.00 0.00 0.00 4.85
1384 1560 2.956987 CTGCAAAGGTGGCCTTCG 59.043 61.111 3.32 0.00 43.92 3.79
1389 1565 3.178540 AAAGGTGGCCTTCGCGTCT 62.179 57.895 5.77 0.00 43.92 4.18
1596 1772 1.685224 CTACAGCCCCTGCCTCAAA 59.315 57.895 0.00 0.00 38.69 2.69
1615 1791 7.235430 CTCAAACGGAGGTGATAATAACTTC 57.765 40.000 0.00 0.00 40.13 3.01
1616 1792 6.703319 TCAAACGGAGGTGATAATAACTTCA 58.297 36.000 0.00 0.00 0.00 3.02
1617 1793 6.816640 TCAAACGGAGGTGATAATAACTTCAG 59.183 38.462 0.00 0.00 0.00 3.02
1618 1794 6.540438 AACGGAGGTGATAATAACTTCAGA 57.460 37.500 0.00 0.00 0.00 3.27
1620 1796 5.421056 ACGGAGGTGATAATAACTTCAGACA 59.579 40.000 0.00 0.00 0.00 3.41
1621 1797 6.098409 ACGGAGGTGATAATAACTTCAGACAT 59.902 38.462 0.00 0.00 0.00 3.06
1622 1798 6.422100 CGGAGGTGATAATAACTTCAGACATG 59.578 42.308 0.00 0.00 0.00 3.21
1623 1799 7.500992 GGAGGTGATAATAACTTCAGACATGA 58.499 38.462 0.00 0.00 0.00 3.07
1625 1801 7.504403 AGGTGATAATAACTTCAGACATGAGG 58.496 38.462 0.00 0.00 38.45 3.86
1626 1802 7.345653 AGGTGATAATAACTTCAGACATGAGGA 59.654 37.037 0.00 0.00 36.10 3.71
1627 1803 8.153550 GGTGATAATAACTTCAGACATGAGGAT 58.846 37.037 0.00 0.00 36.10 3.24
1628 1804 9.553064 GTGATAATAACTTCAGACATGAGGATT 57.447 33.333 0.00 0.00 36.10 3.01
1631 1807 9.911788 ATAATAACTTCAGACATGAGGATTTGT 57.088 29.630 0.00 0.00 36.10 2.83
1633 1809 3.755378 ACTTCAGACATGAGGATTTGTGC 59.245 43.478 0.00 0.00 36.10 4.57
1634 1810 3.421919 TCAGACATGAGGATTTGTGCA 57.578 42.857 0.00 0.00 0.00 4.57
1635 1811 3.340928 TCAGACATGAGGATTTGTGCAG 58.659 45.455 0.00 0.00 0.00 4.41
1636 1812 3.008266 TCAGACATGAGGATTTGTGCAGA 59.992 43.478 0.00 0.00 0.00 4.26
1637 1813 3.374367 CAGACATGAGGATTTGTGCAGAG 59.626 47.826 0.00 0.00 0.00 3.35
1684 1863 4.478203 TGGAGAAGATCGAGAGGATTGAT 58.522 43.478 0.00 0.00 34.82 2.57
1687 1866 5.212532 AGAAGATCGAGAGGATTGATTGG 57.787 43.478 0.00 0.00 34.82 3.16
1690 1869 4.954875 AGATCGAGAGGATTGATTGGAAC 58.045 43.478 0.00 0.00 34.82 3.62
2334 2555 4.351938 TTCAGGTCCCGCGTCGTG 62.352 66.667 4.92 7.40 0.00 4.35
2580 2801 4.486503 CTCCTGCTGGGCCTGCTC 62.487 72.222 31.52 8.82 34.39 4.26
2895 3116 2.370445 CCTCGCCACCCTCCTCATT 61.370 63.158 0.00 0.00 0.00 2.57
2926 3147 2.067616 CAGGTACGCACGTACTTGC 58.932 57.895 25.56 14.03 46.31 4.01
2932 3153 0.666577 ACGCACGTACTTGCTCTTCC 60.667 55.000 20.55 0.00 40.62 3.46
2942 3166 4.001618 ACTTGCTCTTCCTCTTCTTGTC 57.998 45.455 0.00 0.00 0.00 3.18
2950 3174 0.745845 CCTCTTCTTGTCCATGCCGG 60.746 60.000 0.00 0.00 0.00 6.13
2981 3205 2.279517 GGCGAACGGCGATGAGAT 60.280 61.111 16.62 0.00 44.92 2.75
2982 3206 2.589492 GGCGAACGGCGATGAGATG 61.589 63.158 16.62 0.00 44.92 2.90
2983 3207 2.589492 GCGAACGGCGATGAGATGG 61.589 63.158 16.62 0.00 44.57 3.51
2984 3208 1.951130 CGAACGGCGATGAGATGGG 60.951 63.158 16.62 0.00 44.57 4.00
2985 3209 1.441729 GAACGGCGATGAGATGGGA 59.558 57.895 16.62 0.00 0.00 4.37
3389 3613 2.270352 TCACGCCCTTGTGAAAAGAT 57.730 45.000 0.00 0.00 45.40 2.40
3390 3614 1.879380 TCACGCCCTTGTGAAAAGATG 59.121 47.619 0.00 0.00 45.40 2.90
3391 3615 1.879380 CACGCCCTTGTGAAAAGATGA 59.121 47.619 0.00 0.00 42.55 2.92
3392 3616 2.293122 CACGCCCTTGTGAAAAGATGAA 59.707 45.455 0.00 0.00 42.55 2.57
3393 3617 2.293399 ACGCCCTTGTGAAAAGATGAAC 59.707 45.455 0.00 0.00 0.00 3.18
3394 3618 2.351738 CGCCCTTGTGAAAAGATGAACC 60.352 50.000 0.00 0.00 0.00 3.62
3395 3619 2.627699 GCCCTTGTGAAAAGATGAACCA 59.372 45.455 0.00 0.00 0.00 3.67
3396 3620 3.259123 GCCCTTGTGAAAAGATGAACCAT 59.741 43.478 0.00 0.00 0.00 3.55
3404 3638 4.523943 TGAAAAGATGAACCATGGGAGTTG 59.476 41.667 18.09 0.00 0.00 3.16
3481 3719 5.127693 TGCATGTTTGTTAATGGGTACAC 57.872 39.130 0.00 0.00 0.00 2.90
3487 3725 3.530265 TGTTAATGGGTACACGCCTAG 57.470 47.619 0.00 0.00 0.00 3.02
3541 3779 7.491372 GGGTTTTCTTCTTGTTTGTTTCCTTAG 59.509 37.037 0.00 0.00 0.00 2.18
3552 3790 4.561735 TGTTTCCTTAGTTTTCCTTGCG 57.438 40.909 0.00 0.00 0.00 4.85
3599 3837 1.152881 GTGGCCCAAGCTATCCCAG 60.153 63.158 0.00 0.00 39.73 4.45
3666 3904 2.364970 TGTGCATGGGTTTTCTTCTTGG 59.635 45.455 0.00 0.00 0.00 3.61
3681 3919 8.770010 TTTCTTCTTGGTGGTTTCCTTAATAA 57.230 30.769 0.00 0.00 0.00 1.40
3711 3949 5.940470 AGTTTTGCTATTTCTCAGGTACCTG 59.060 40.000 32.61 32.61 44.86 4.00
3757 3998 2.767505 TCTTTCTTCCTTCCTTCACGC 58.232 47.619 0.00 0.00 0.00 5.34
3874 4119 0.334676 TATCTTTGGGGGTGCAAGGG 59.665 55.000 0.00 0.00 0.00 3.95
3876 4121 4.247130 TTTGGGGGTGCAAGGGGG 62.247 66.667 0.00 0.00 0.00 5.40
3880 4125 4.994756 GGGGTGCAAGGGGGTGTG 62.995 72.222 0.00 0.00 0.00 3.82
3881 4126 4.218686 GGGTGCAAGGGGGTGTGT 62.219 66.667 0.00 0.00 0.00 3.72
3882 4127 2.836187 GGGTGCAAGGGGGTGTGTA 61.836 63.158 0.00 0.00 0.00 2.90
3883 4128 1.382629 GGTGCAAGGGGGTGTGTAT 59.617 57.895 0.00 0.00 0.00 2.29
3884 4129 0.965363 GGTGCAAGGGGGTGTGTATG 60.965 60.000 0.00 0.00 0.00 2.39
3885 4130 0.251165 GTGCAAGGGGGTGTGTATGT 60.251 55.000 0.00 0.00 0.00 2.29
3886 4131 0.251121 TGCAAGGGGGTGTGTATGTG 60.251 55.000 0.00 0.00 0.00 3.21
3887 4132 0.251165 GCAAGGGGGTGTGTATGTGT 60.251 55.000 0.00 0.00 0.00 3.72
3888 4133 1.533625 CAAGGGGGTGTGTATGTGTG 58.466 55.000 0.00 0.00 0.00 3.82
3889 4134 1.145571 AAGGGGGTGTGTATGTGTGT 58.854 50.000 0.00 0.00 0.00 3.72
3890 4135 0.400213 AGGGGGTGTGTATGTGTGTG 59.600 55.000 0.00 0.00 0.00 3.82
3891 4136 0.109723 GGGGGTGTGTATGTGTGTGT 59.890 55.000 0.00 0.00 0.00 3.72
3892 4137 1.234821 GGGGTGTGTATGTGTGTGTG 58.765 55.000 0.00 0.00 0.00 3.82
3893 4138 1.202710 GGGGTGTGTATGTGTGTGTGA 60.203 52.381 0.00 0.00 0.00 3.58
3894 4139 2.552155 GGGGTGTGTATGTGTGTGTGAT 60.552 50.000 0.00 0.00 0.00 3.06
3895 4140 3.307129 GGGGTGTGTATGTGTGTGTGATA 60.307 47.826 0.00 0.00 0.00 2.15
3896 4141 3.932710 GGGTGTGTATGTGTGTGTGATAG 59.067 47.826 0.00 0.00 0.00 2.08
3915 4161 5.246203 TGATAGCCCACAAGTATAGGTGATC 59.754 44.000 0.00 0.00 37.18 2.92
3918 4164 3.431766 GCCCACAAGTATAGGTGATCGTT 60.432 47.826 0.00 0.00 37.18 3.85
3920 4166 5.682990 GCCCACAAGTATAGGTGATCGTTTA 60.683 44.000 0.00 0.00 37.18 2.01
3925 4171 7.865889 CACAAGTATAGGTGATCGTTTATAGCA 59.134 37.037 0.00 0.00 37.18 3.49
3957 4206 4.419522 AAAAATGTCGAATCCAACGAGG 57.580 40.909 0.00 0.00 40.37 4.63
3969 4218 2.494870 TCCAACGAGGAGCTAAAGGTAC 59.505 50.000 0.00 0.00 43.07 3.34
4002 4251 4.809958 TCTCTCAAGTTCTATCGACTACCG 59.190 45.833 0.00 0.00 40.25 4.02
4025 4274 1.134640 ACAACTCTACGCACACCAACA 60.135 47.619 0.00 0.00 0.00 3.33
4080 4329 9.886132 ATTAGAAGTATTTTGTAGGTGTAGTGG 57.114 33.333 0.00 0.00 0.00 4.00
4086 4335 8.999895 AGTATTTTGTAGGTGTAGTGGGATAAT 58.000 33.333 0.00 0.00 0.00 1.28
4100 4349 9.683069 GTAGTGGGATAATTTTGCAAGATAATG 57.317 33.333 2.45 0.00 0.00 1.90
4177 4426 0.669318 TAGCGAGCGTGGAAAAGTGG 60.669 55.000 0.00 0.00 0.00 4.00
4180 4429 1.504359 CGAGCGTGGAAAAGTGGTAA 58.496 50.000 0.00 0.00 0.00 2.85
4183 4432 3.680937 CGAGCGTGGAAAAGTGGTAATAA 59.319 43.478 0.00 0.00 0.00 1.40
4189 4438 7.039993 AGCGTGGAAAAGTGGTAATAAGATTTT 60.040 33.333 0.00 0.00 0.00 1.82
4190 4439 7.061789 GCGTGGAAAAGTGGTAATAAGATTTTG 59.938 37.037 0.00 0.00 0.00 2.44
4191 4440 8.293867 CGTGGAAAAGTGGTAATAAGATTTTGA 58.706 33.333 0.00 0.00 0.00 2.69
4228 4477 4.671766 GCAATTGGCTTTGTTACTAGACCG 60.672 45.833 7.72 0.00 40.25 4.79
4231 4480 3.164268 TGGCTTTGTTACTAGACCGGTA 58.836 45.455 7.34 0.00 0.00 4.02
4242 4491 4.756502 ACTAGACCGGTAGCAAATTCTTC 58.243 43.478 7.34 0.00 0.00 2.87
4282 4531 5.118990 GCTAGCATGTCATTCCTTACTTGA 58.881 41.667 10.63 0.00 0.00 3.02
4335 4584 4.339247 AGCAAGCATCCGCAACTATTAAAT 59.661 37.500 0.00 0.00 42.27 1.40
4342 4591 8.629158 AGCATCCGCAACTATTAAATTTCATTA 58.371 29.630 0.00 0.00 42.27 1.90
4345 4594 9.965824 ATCCGCAACTATTAAATTTCATTAAGG 57.034 29.630 0.00 0.00 0.00 2.69
4361 4610 7.948034 TCATTAAGGTAAAACCCAACCATAG 57.052 36.000 0.00 0.00 39.75 2.23
4362 4611 6.378848 TCATTAAGGTAAAACCCAACCATAGC 59.621 38.462 0.00 0.00 39.75 2.97
4363 4612 3.818295 AGGTAAAACCCAACCATAGCA 57.182 42.857 0.00 0.00 39.75 3.49
4364 4613 4.331159 AGGTAAAACCCAACCATAGCAT 57.669 40.909 0.00 0.00 39.75 3.79
4365 4614 4.683643 AGGTAAAACCCAACCATAGCATT 58.316 39.130 0.00 0.00 39.75 3.56
4366 4615 5.833340 AGGTAAAACCCAACCATAGCATTA 58.167 37.500 0.00 0.00 39.75 1.90
4367 4616 6.257586 AGGTAAAACCCAACCATAGCATTAA 58.742 36.000 0.00 0.00 39.75 1.40
4368 4617 6.379988 AGGTAAAACCCAACCATAGCATTAAG 59.620 38.462 0.00 0.00 39.75 1.85
4369 4618 6.378848 GGTAAAACCCAACCATAGCATTAAGA 59.621 38.462 0.00 0.00 35.73 2.10
4370 4619 7.069455 GGTAAAACCCAACCATAGCATTAAGAT 59.931 37.037 0.00 0.00 35.73 2.40
4371 4620 9.127277 GTAAAACCCAACCATAGCATTAAGATA 57.873 33.333 0.00 0.00 0.00 1.98
4372 4621 8.782137 AAAACCCAACCATAGCATTAAGATAT 57.218 30.769 0.00 0.00 0.00 1.63
4373 4622 9.875708 AAAACCCAACCATAGCATTAAGATATA 57.124 29.630 0.00 0.00 0.00 0.86
4376 4625 9.466497 ACCCAACCATAGCATTAAGATATATTG 57.534 33.333 0.00 0.00 0.00 1.90
4377 4626 8.906867 CCCAACCATAGCATTAAGATATATTGG 58.093 37.037 0.00 0.00 40.40 3.16
4378 4627 9.466497 CCAACCATAGCATTAAGATATATTGGT 57.534 33.333 0.00 0.00 38.25 3.67
4380 4629 9.686683 AACCATAGCATTAAGATATATTGGTCC 57.313 33.333 0.00 0.00 0.00 4.46
4381 4630 8.275040 ACCATAGCATTAAGATATATTGGTCCC 58.725 37.037 0.00 0.00 0.00 4.46
4382 4631 7.721399 CCATAGCATTAAGATATATTGGTCCCC 59.279 40.741 0.00 0.00 0.00 4.81
4383 4632 6.977244 AGCATTAAGATATATTGGTCCCCT 57.023 37.500 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
156 157 0.178767 TCGATATTGCACTGCCAGCT 59.821 50.000 0.00 0.00 0.00 4.24
197 198 2.902705 TCTTGCAAACCGTGTCTAGT 57.097 45.000 0.00 0.00 0.00 2.57
217 218 7.011576 TCACAAAAGTAGCATTTAGACGTTTGA 59.988 33.333 15.96 0.00 41.85 2.69
258 259 0.107643 TTGCAAGATGTGGTCGACCA 59.892 50.000 33.23 33.23 45.30 4.02
286 287 5.057149 GTGTACCACACTTGTCTTGAGAAT 58.943 41.667 2.22 0.00 45.27 2.40
309 310 0.184211 TCCCATCCTGGTCATGCATG 59.816 55.000 21.07 21.07 35.17 4.06
499 500 7.466804 AGTCCACAGTCTCCCATTTATTTTTA 58.533 34.615 0.00 0.00 0.00 1.52
506 507 2.711009 TCAAGTCCACAGTCTCCCATTT 59.289 45.455 0.00 0.00 0.00 2.32
570 571 1.213926 ACTCGGGTATAGGTCGTCCTT 59.786 52.381 6.51 0.00 42.12 3.36
622 624 2.672996 CAAGCCGACCCCAACCAG 60.673 66.667 0.00 0.00 0.00 4.00
649 651 6.338146 ACAAGAGTTATTACATTGCGCTAGA 58.662 36.000 9.73 0.00 30.56 2.43
685 688 7.344095 AGCGTACCTTAGCTTTATAGAAAGA 57.656 36.000 13.94 0.00 44.23 2.52
687 690 9.472361 CAATAGCGTACCTTAGCTTTATAGAAA 57.528 33.333 0.00 0.00 44.15 2.52
777 780 1.574263 ACCTTCCACTCTAGAAGCCC 58.426 55.000 0.00 0.00 39.55 5.19
854 859 6.306199 ACTTTGTTACCGGGTATTTTTACCT 58.694 36.000 7.90 0.00 39.97 3.08
909 914 1.661341 AGAAATCGCATGACAGGAGC 58.339 50.000 0.00 0.00 0.00 4.70
938 943 4.511826 CGGCCGCTCTCTTCTTTTTATTAT 59.488 41.667 14.67 0.00 0.00 1.28
939 944 3.869246 CGGCCGCTCTCTTCTTTTTATTA 59.131 43.478 14.67 0.00 0.00 0.98
940 945 2.678336 CGGCCGCTCTCTTCTTTTTATT 59.322 45.455 14.67 0.00 0.00 1.40
997 1007 2.252346 CGCTGCTGATCTCCATGGC 61.252 63.158 6.96 0.00 0.00 4.40
1032 1042 1.153549 GAGGTGCTCCACGATGGAC 60.154 63.158 7.70 2.56 42.67 4.02
1101 1111 1.939980 ATATAGGAAGAGGGCCGTCC 58.060 55.000 21.60 12.98 42.79 4.79
1164 1206 9.883142 AATTTTGAAAGAAGTGTATGGTGAAAA 57.117 25.926 0.00 0.00 0.00 2.29
1193 1237 9.601217 CTACTAAACATAATCCACTGCTACTTT 57.399 33.333 0.00 0.00 0.00 2.66
1195 1239 8.534954 TCTACTAAACATAATCCACTGCTACT 57.465 34.615 0.00 0.00 0.00 2.57
1197 1241 9.197306 TCTTCTACTAAACATAATCCACTGCTA 57.803 33.333 0.00 0.00 0.00 3.49
1198 1242 8.079211 TCTTCTACTAAACATAATCCACTGCT 57.921 34.615 0.00 0.00 0.00 4.24
1210 1254 8.149973 AGCGAAAATGTTTCTTCTACTAAACA 57.850 30.769 3.40 3.40 46.37 2.83
1212 1256 8.495949 CAGAGCGAAAATGTTTCTTCTACTAAA 58.504 33.333 0.00 0.00 0.00 1.85
1213 1257 7.360101 GCAGAGCGAAAATGTTTCTTCTACTAA 60.360 37.037 0.00 0.00 0.00 2.24
1214 1258 6.090898 GCAGAGCGAAAATGTTTCTTCTACTA 59.909 38.462 0.00 0.00 0.00 1.82
1244 1420 7.067008 CCCCGTTACATGTCATAAAAAGAGAAT 59.933 37.037 0.00 0.00 0.00 2.40
1249 1425 4.398044 AGCCCCGTTACATGTCATAAAAAG 59.602 41.667 0.00 0.00 0.00 2.27
1250 1426 4.337145 AGCCCCGTTACATGTCATAAAAA 58.663 39.130 0.00 0.00 0.00 1.94
1251 1427 3.942748 GAGCCCCGTTACATGTCATAAAA 59.057 43.478 0.00 0.00 0.00 1.52
1252 1428 3.199071 AGAGCCCCGTTACATGTCATAAA 59.801 43.478 0.00 0.00 0.00 1.40
1267 1443 0.254178 TTTCTCATGAGCAGAGCCCC 59.746 55.000 18.36 0.00 33.15 5.80
1269 1445 2.613133 GTGATTTCTCATGAGCAGAGCC 59.387 50.000 18.36 5.45 32.98 4.70
1286 1462 2.269023 TCCATCCACAGACAAGGTGAT 58.731 47.619 0.00 0.00 38.54 3.06
1296 1472 3.947910 AACTGCATTTTCCATCCACAG 57.052 42.857 0.00 0.00 0.00 3.66
1345 1521 2.283173 CAGGGGGTTCTTGGCACC 60.283 66.667 0.00 0.00 0.00 5.01
1384 1560 1.448540 CCACCCTCATGTGAGACGC 60.449 63.158 11.47 0.00 44.74 5.19
1389 1565 1.491754 CCATGATCCACCCTCATGTGA 59.508 52.381 11.19 0.00 45.52 3.58
1596 1772 5.421056 TGTCTGAAGTTATTATCACCTCCGT 59.579 40.000 0.00 0.00 0.00 4.69
1606 1782 9.166173 CACAAATCCTCATGTCTGAAGTTATTA 57.834 33.333 0.00 0.00 0.00 0.98
1609 1785 5.412594 GCACAAATCCTCATGTCTGAAGTTA 59.587 40.000 0.00 0.00 0.00 2.24
1611 1787 3.755378 GCACAAATCCTCATGTCTGAAGT 59.245 43.478 0.00 0.00 0.00 3.01
1612 1788 3.754850 TGCACAAATCCTCATGTCTGAAG 59.245 43.478 0.00 0.00 0.00 3.02
1613 1789 3.753815 TGCACAAATCCTCATGTCTGAA 58.246 40.909 0.00 0.00 0.00 3.02
1614 1790 3.008266 TCTGCACAAATCCTCATGTCTGA 59.992 43.478 0.00 0.00 0.00 3.27
1615 1791 3.340928 TCTGCACAAATCCTCATGTCTG 58.659 45.455 0.00 0.00 0.00 3.51
1616 1792 3.008813 ACTCTGCACAAATCCTCATGTCT 59.991 43.478 0.00 0.00 0.00 3.41
1617 1793 3.341823 ACTCTGCACAAATCCTCATGTC 58.658 45.455 0.00 0.00 0.00 3.06
1618 1794 3.430042 ACTCTGCACAAATCCTCATGT 57.570 42.857 0.00 0.00 0.00 3.21
1620 1796 4.298103 AGAACTCTGCACAAATCCTCAT 57.702 40.909 0.00 0.00 0.00 2.90
1621 1797 3.777106 AGAACTCTGCACAAATCCTCA 57.223 42.857 0.00 0.00 0.00 3.86
1622 1798 3.365767 GCAAGAACTCTGCACAAATCCTC 60.366 47.826 0.00 0.00 0.00 3.71
1623 1799 2.555757 GCAAGAACTCTGCACAAATCCT 59.444 45.455 0.00 0.00 0.00 3.24
1625 1801 2.578495 CGCAAGAACTCTGCACAAATC 58.422 47.619 0.00 0.00 43.02 2.17
1626 1802 2.693797 CGCAAGAACTCTGCACAAAT 57.306 45.000 0.00 0.00 43.02 2.32
1635 1811 8.897738 TTGTTCTACAAGGAATCGCAAGAACTC 61.898 40.741 12.06 0.00 41.29 3.01
1636 1812 7.184863 TTGTTCTACAAGGAATCGCAAGAACT 61.185 38.462 12.06 0.00 41.29 3.01
1637 1813 5.049680 TTGTTCTACAAGGAATCGCAAGAAC 60.050 40.000 0.00 0.00 41.29 3.01
1684 1863 2.161808 TCGCAACGAACAAAAGTTCCAA 59.838 40.909 3.07 0.00 31.06 3.53
1687 1866 4.736562 CATTTCGCAACGAACAAAAGTTC 58.263 39.130 1.28 0.00 45.64 3.01
1690 1869 3.140281 GCATTTCGCAACGAACAAAAG 57.860 42.857 1.28 0.00 45.64 2.27
2334 2555 4.715523 TTGGCCTGCAGGTACGCC 62.716 66.667 32.81 26.42 41.99 5.68
2343 2564 1.377333 GTCCCTGTACTTGGCCTGC 60.377 63.158 3.32 0.00 0.00 4.85
2571 2792 3.635268 CTTCCACCAGAGCAGGCCC 62.635 68.421 0.00 0.00 0.00 5.80
2577 2798 1.739562 CTGCGACTTCCACCAGAGC 60.740 63.158 0.00 0.00 0.00 4.09
2580 2801 1.734477 CGTCTGCGACTTCCACCAG 60.734 63.158 7.03 0.00 41.33 4.00
2916 3137 3.057174 AGAAGAGGAAGAGCAAGTACGTG 60.057 47.826 4.24 4.24 0.00 4.49
2925 3146 3.269178 CATGGACAAGAAGAGGAAGAGC 58.731 50.000 0.00 0.00 0.00 4.09
2926 3147 3.269178 GCATGGACAAGAAGAGGAAGAG 58.731 50.000 0.00 0.00 0.00 2.85
2932 3153 1.372087 GCCGGCATGGACAAGAAGAG 61.372 60.000 24.80 0.00 42.00 2.85
2981 3205 2.456577 TGATCACAGATCGAACTCCCA 58.543 47.619 0.00 0.00 0.00 4.37
2982 3206 3.068732 TGATGATCACAGATCGAACTCCC 59.931 47.826 0.00 0.00 0.00 4.30
2983 3207 4.297510 CTGATGATCACAGATCGAACTCC 58.702 47.826 15.93 0.00 37.54 3.85
2984 3208 4.297510 CCTGATGATCACAGATCGAACTC 58.702 47.826 20.26 3.49 37.54 3.01
2985 3209 3.069300 CCCTGATGATCACAGATCGAACT 59.931 47.826 20.26 0.00 37.54 3.01
3389 3613 1.076549 GCCCAACTCCCATGGTTCA 59.923 57.895 11.73 0.00 36.14 3.18
3390 3614 1.076549 TGCCCAACTCCCATGGTTC 59.923 57.895 11.73 0.00 36.14 3.62
3391 3615 1.228862 GTGCCCAACTCCCATGGTT 60.229 57.895 11.73 0.00 36.14 3.67
3392 3616 2.440599 GTGCCCAACTCCCATGGT 59.559 61.111 11.73 0.00 36.14 3.55
3393 3617 2.751436 CGTGCCCAACTCCCATGG 60.751 66.667 4.14 4.14 37.71 3.66
3394 3618 2.751436 CCGTGCCCAACTCCCATG 60.751 66.667 0.00 0.00 0.00 3.66
3395 3619 4.740822 GCCGTGCCCAACTCCCAT 62.741 66.667 0.00 0.00 0.00 4.00
3487 3725 0.320771 TGCTCTCGGTTCTTGCCTTC 60.321 55.000 0.00 0.00 0.00 3.46
3499 3737 1.028330 ACCCATGCACATTGCTCTCG 61.028 55.000 0.00 0.00 45.31 4.04
3541 3779 1.886886 TACCTCCACGCAAGGAAAAC 58.113 50.000 5.42 0.00 46.39 2.43
3552 3790 2.019156 GCAAGGCCTCATTACCTCCAC 61.019 57.143 5.23 0.00 34.31 4.02
3681 3919 6.944862 ACCTGAGAAATAGCAAAACTGAAGAT 59.055 34.615 0.00 0.00 0.00 2.40
3726 3967 7.641249 AGGAAGGAAGAAAGAAGATGATTGAT 58.359 34.615 0.00 0.00 0.00 2.57
3731 3972 6.234177 GTGAAGGAAGGAAGAAAGAAGATGA 58.766 40.000 0.00 0.00 0.00 2.92
3734 3975 4.632153 CGTGAAGGAAGGAAGAAAGAAGA 58.368 43.478 0.00 0.00 0.00 2.87
3874 4119 2.248280 TCACACACACATACACACCC 57.752 50.000 0.00 0.00 0.00 4.61
3876 4121 3.370978 GGCTATCACACACACATACACAC 59.629 47.826 0.00 0.00 0.00 3.82
3877 4122 3.595173 GGCTATCACACACACATACACA 58.405 45.455 0.00 0.00 0.00 3.72
3878 4123 2.936498 GGGCTATCACACACACATACAC 59.064 50.000 0.00 0.00 0.00 2.90
3879 4124 2.569404 TGGGCTATCACACACACATACA 59.431 45.455 0.00 0.00 0.00 2.29
3880 4125 2.936498 GTGGGCTATCACACACACATAC 59.064 50.000 0.00 0.00 37.54 2.39
3881 4126 2.569404 TGTGGGCTATCACACACACATA 59.431 45.455 0.00 0.00 42.20 2.29
3882 4127 1.350684 TGTGGGCTATCACACACACAT 59.649 47.619 0.00 0.00 42.20 3.21
3883 4128 0.761802 TGTGGGCTATCACACACACA 59.238 50.000 0.00 0.00 42.20 3.72
3884 4129 1.806542 CTTGTGGGCTATCACACACAC 59.193 52.381 0.02 0.00 46.25 3.82
3885 4130 1.419762 ACTTGTGGGCTATCACACACA 59.580 47.619 0.02 0.00 46.25 3.72
3886 4131 2.185004 ACTTGTGGGCTATCACACAC 57.815 50.000 0.02 0.00 46.25 3.82
3887 4132 4.100963 CCTATACTTGTGGGCTATCACACA 59.899 45.833 0.00 0.00 45.95 3.72
3888 4133 4.101119 ACCTATACTTGTGGGCTATCACAC 59.899 45.833 7.39 0.00 45.95 3.82
3889 4134 4.100963 CACCTATACTTGTGGGCTATCACA 59.899 45.833 4.47 4.47 44.81 3.58
3890 4135 4.344102 TCACCTATACTTGTGGGCTATCAC 59.656 45.833 0.00 0.00 38.09 3.06
3891 4136 4.552674 TCACCTATACTTGTGGGCTATCA 58.447 43.478 0.00 0.00 33.29 2.15
3892 4137 5.622460 CGATCACCTATACTTGTGGGCTATC 60.622 48.000 0.00 0.00 33.29 2.08
3893 4138 4.220821 CGATCACCTATACTTGTGGGCTAT 59.779 45.833 0.00 0.00 33.29 2.97
3894 4139 3.572682 CGATCACCTATACTTGTGGGCTA 59.427 47.826 0.00 0.00 33.29 3.93
3895 4140 2.365617 CGATCACCTATACTTGTGGGCT 59.634 50.000 0.00 0.00 33.29 5.19
3896 4141 2.102588 ACGATCACCTATACTTGTGGGC 59.897 50.000 0.00 0.00 33.29 5.36
3937 4183 3.670625 TCCTCGTTGGATTCGACATTTT 58.329 40.909 0.00 0.00 40.56 1.82
3938 4184 3.262420 CTCCTCGTTGGATTCGACATTT 58.738 45.455 0.00 0.00 45.16 2.32
3998 4247 3.009026 TGTGCGTAGAGTTGTATCGGTA 58.991 45.455 0.00 0.00 0.00 4.02
4000 4249 2.182825 GTGTGCGTAGAGTTGTATCGG 58.817 52.381 0.00 0.00 0.00 4.18
4002 4251 3.226346 TGGTGTGCGTAGAGTTGTATC 57.774 47.619 0.00 0.00 0.00 2.24
4025 4274 8.788325 ATTACTTGTTTCTAGGTAAAGCGAAT 57.212 30.769 0.00 0.00 0.00 3.34
4086 4335 9.761504 TTTCATGTTCTTCATTATCTTGCAAAA 57.238 25.926 0.00 0.00 34.09 2.44
4141 4390 8.131100 ACGCTCGCTATACTAACTTAATTGTTA 58.869 33.333 0.00 0.00 0.00 2.41
4142 4391 6.976925 ACGCTCGCTATACTAACTTAATTGTT 59.023 34.615 0.00 0.00 0.00 2.83
4165 4414 8.293867 TCAAAATCTTATTACCACTTTTCCACG 58.706 33.333 0.00 0.00 0.00 4.94
4180 4429 8.907885 GCTTAGGGACAATTCTCAAAATCTTAT 58.092 33.333 0.00 0.00 0.00 1.73
4183 4432 6.248433 TGCTTAGGGACAATTCTCAAAATCT 58.752 36.000 0.00 0.00 0.00 2.40
4189 4438 4.706476 CCAATTGCTTAGGGACAATTCTCA 59.294 41.667 0.00 0.00 42.93 3.27
4190 4439 4.440663 GCCAATTGCTTAGGGACAATTCTC 60.441 45.833 0.00 0.00 42.93 2.87
4191 4440 3.448660 GCCAATTGCTTAGGGACAATTCT 59.551 43.478 0.00 0.00 42.93 2.40
4228 4477 4.141251 TCCCCCATAGAAGAATTTGCTACC 60.141 45.833 0.00 0.00 0.00 3.18
4231 4480 3.117360 CCTCCCCCATAGAAGAATTTGCT 60.117 47.826 0.00 0.00 0.00 3.91
4242 4491 3.125376 GCAGTGGCCTCCCCCATAG 62.125 68.421 3.32 0.00 37.20 2.23
4299 4548 6.498304 CGGATGCTTGCTAATAGTTTCAATT 58.502 36.000 0.00 0.00 0.00 2.32
4319 4568 9.965824 CCTTAATGAAATTTAATAGTTGCGGAT 57.034 29.630 0.00 0.00 37.87 4.18
4335 4584 7.619512 ATGGTTGGGTTTTACCTTAATGAAA 57.380 32.000 0.00 0.00 38.64 2.69
4342 4591 4.120946 TGCTATGGTTGGGTTTTACCTT 57.879 40.909 0.00 0.00 38.64 3.50
4345 4594 7.399245 TCTTAATGCTATGGTTGGGTTTTAC 57.601 36.000 0.00 0.00 0.00 2.01


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

AutoCloner maintained by Alex Coulton.