Multiple sequence alignment - TraesCS7A01G438400

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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 TraesCS7A01G438400 chr7A 100.000 2471 0 0 1 2471 632552114 632549644 0.000000e+00 4564.0
1 TraesCS7A01G438400 chr7A 91.353 902 48 12 938 1830 632526569 632527449 0.000000e+00 1206.0
2 TraesCS7A01G438400 chr7A 92.298 805 40 12 784 1570 632531889 632532689 0.000000e+00 1123.0
3 TraesCS7A01G438400 chr7A 90.439 774 42 10 1 748 167742602 167741835 0.000000e+00 990.0
4 TraesCS7A01G438400 chr7A 85.093 644 54 13 140 748 85187022 85186386 9.710000e-174 619.0
5 TraesCS7A01G438400 chr7A 89.918 486 40 1 979 1455 100063774 100064259 3.490000e-173 617.0
6 TraesCS7A01G438400 chr7A 85.430 151 19 3 599 748 608221849 608221997 1.180000e-33 154.0
7 TraesCS7A01G438400 chr7A 89.474 76 7 1 2320 2394 632545480 632545405 7.270000e-16 95.3
8 TraesCS7A01G438400 chr7B 91.956 1007 63 10 795 1790 591949318 591950317 0.000000e+00 1395.0
9 TraesCS7A01G438400 chr7B 89.267 1118 86 15 746 1861 592348607 592347522 0.000000e+00 1369.0
10 TraesCS7A01G438400 chr7B 90.223 808 49 24 784 1573 592355554 592354759 0.000000e+00 1027.0
11 TraesCS7A01G438400 chr7B 91.632 729 44 7 784 1495 591723711 591724439 0.000000e+00 992.0
12 TraesCS7A01G438400 chr7B 86.386 808 62 20 802 1570 591713253 591714051 0.000000e+00 839.0
13 TraesCS7A01G438400 chr7B 89.366 489 42 4 140 619 679110464 679110951 7.560000e-170 606.0
14 TraesCS7A01G438400 chr7B 84.019 632 69 21 140 750 624355232 624354612 1.650000e-161 579.0
15 TraesCS7A01G438400 chr7B 85.768 267 22 10 1570 1831 592354861 592354606 4.050000e-68 268.0
16 TraesCS7A01G438400 chr7B 97.590 83 2 0 1965 2047 591950524 591950606 2.560000e-30 143.0
17 TraesCS7A01G438400 chr7B 92.857 98 6 1 2156 2253 465970487 465970583 9.210000e-30 141.0
18 TraesCS7A01G438400 chr7B 86.842 76 9 1 2320 2394 592342424 592342349 1.570000e-12 84.2
19 TraesCS7A01G438400 chr7D 89.950 995 72 18 781 1772 548776824 548775855 0.000000e+00 1258.0
20 TraesCS7A01G438400 chr7D 92.437 714 40 9 780 1493 548782243 548781544 0.000000e+00 1007.0
21 TraesCS7A01G438400 chr7D 90.014 721 50 10 796 1495 548708853 548709572 0.000000e+00 913.0
22 TraesCS7A01G438400 chr7D 88.547 716 50 14 802 1495 548696962 548697667 0.000000e+00 839.0
23 TraesCS7A01G438400 chr7D 93.233 133 8 1 2047 2179 548775485 548775354 6.970000e-46 195.0
24 TraesCS7A01G438400 chr7D 80.423 189 21 6 1570 1751 548781552 548781373 1.990000e-26 130.0
25 TraesCS7A01G438400 chr7D 84.746 118 2 3 2370 2471 548775009 548774892 1.210000e-18 104.0
26 TraesCS7A01G438400 chr7D 95.833 48 2 0 2002 2049 548775570 548775523 7.330000e-11 78.7
27 TraesCS7A01G438400 chr2A 91.053 760 46 8 1 744 158032883 158033636 0.000000e+00 1007.0
28 TraesCS7A01G438400 chr2A 89.310 580 35 10 188 744 713229300 713228725 0.000000e+00 702.0
29 TraesCS7A01G438400 chr2A 85.174 634 57 12 147 747 746929972 746930601 1.260000e-172 616.0
30 TraesCS7A01G438400 chr2A 95.506 89 4 0 1 89 12649578 12649666 2.560000e-30 143.0
31 TraesCS7A01G438400 chr2A 95.506 89 3 1 2165 2253 68249094 68249007 9.210000e-30 141.0
32 TraesCS7A01G438400 chr1A 91.230 764 32 13 1 742 42197164 42196414 0.000000e+00 1007.0
33 TraesCS7A01G438400 chr1A 89.868 760 40 17 1 742 41373273 41372533 0.000000e+00 942.0
34 TraesCS7A01G438400 chr1A 84.112 642 50 21 140 746 451855875 451855251 7.670000e-160 573.0
35 TraesCS7A01G438400 chr1A 89.571 163 17 0 1063 1225 20998188 20998350 8.960000e-50 207.0
36 TraesCS7A01G438400 chr1A 84.729 203 26 4 1024 1225 21022811 21023009 5.390000e-47 198.0
37 TraesCS7A01G438400 chr1A 85.256 156 19 4 599 751 575516771 575516925 9.150000e-35 158.0
38 TraesCS7A01G438400 chr5A 90.674 772 43 10 1 744 568621472 568620702 0.000000e+00 1000.0
39 TraesCS7A01G438400 chr5A 90.814 762 42 13 1 744 566617857 566618608 0.000000e+00 994.0
40 TraesCS7A01G438400 chr5A 89.077 769 52 15 1 744 467368854 467368093 0.000000e+00 926.0
41 TraesCS7A01G438400 chr5A 87.102 628 43 18 140 744 561113759 561114371 0.000000e+00 676.0
42 TraesCS7A01G438400 chr5A 82.166 628 64 10 147 748 588410080 588410685 1.710000e-136 496.0
43 TraesCS7A01G438400 chr5A 93.069 101 5 2 2155 2254 113799762 113799663 1.980000e-31 147.0
44 TraesCS7A01G438400 chr6A 89.714 768 47 14 1 744 614241093 614241852 0.000000e+00 952.0
45 TraesCS7A01G438400 chr3A 90.463 713 47 12 51 747 552467052 552466345 0.000000e+00 920.0
46 TraesCS7A01G438400 chr3A 84.351 639 49 17 147 747 704457901 704458526 1.650000e-161 579.0
47 TraesCS7A01G438400 chr3A 84.146 246 15 8 522 744 16704204 16704448 1.490000e-52 217.0
48 TraesCS7A01G438400 chr2B 84.351 639 62 11 140 744 21456779 21457413 2.120000e-165 592.0
49 TraesCS7A01G438400 chr2B 87.243 486 55 5 140 619 237316634 237317118 4.650000e-152 547.0
50 TraesCS7A01G438400 chrUn 88.017 484 53 3 140 619 274799670 274800152 3.570000e-158 568.0
51 TraesCS7A01G438400 chr4B 88.017 484 53 3 140 619 6402594 6403076 3.570000e-158 568.0
52 TraesCS7A01G438400 chr4B 80.723 83 15 1 802 883 436102358 436102440 2.050000e-06 63.9
53 TraesCS7A01G438400 chr5B 87.000 500 44 10 140 619 542697501 542697003 6.010000e-151 544.0
54 TraesCS7A01G438400 chr5B 94.737 95 4 1 2160 2254 45261727 45261634 1.980000e-31 147.0
55 TraesCS7A01G438400 chr6D 89.506 162 17 0 1064 1225 16502931 16503092 3.220000e-49 206.0
56 TraesCS7A01G438400 chr6D 90.260 154 15 0 1072 1225 16307218 16307065 4.170000e-48 202.0
57 TraesCS7A01G438400 chr6D 88.889 162 18 0 1064 1225 16510778 16510939 1.500000e-47 200.0
58 TraesCS7A01G438400 chr6D 88.889 162 18 0 1064 1225 24001596 24001757 1.500000e-47 200.0
59 TraesCS7A01G438400 chr6D 88.272 162 19 0 1064 1225 16390068 16389907 6.970000e-46 195.0
60 TraesCS7A01G438400 chr6D 88.272 162 19 0 1064 1225 16523159 16522998 6.970000e-46 195.0
61 TraesCS7A01G438400 chr6D 88.272 162 19 0 1064 1225 29089724 29089885 6.970000e-46 195.0
62 TraesCS7A01G438400 chr1D 84.236 203 27 4 1024 1225 19185041 19185239 2.510000e-45 193.0
63 TraesCS7A01G438400 chr1D 95.556 90 3 1 2164 2253 474055679 474055591 2.560000e-30 143.0
64 TraesCS7A01G438400 chr1D 94.565 92 3 2 2167 2257 69615614 69615704 9.210000e-30 141.0
65 TraesCS7A01G438400 chr4D 89.744 117 9 3 2164 2280 98447964 98448077 1.980000e-31 147.0
66 TraesCS7A01G438400 chr4D 93.617 94 4 2 2166 2258 16403538 16403446 3.310000e-29 139.0
67 TraesCS7A01G438400 chr4D 82.278 79 14 0 802 880 352579784 352579862 4.410000e-08 69.4
68 TraesCS7A01G438400 chr1B 91.262 103 7 2 2159 2260 589493108 589493209 3.310000e-29 139.0


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 TraesCS7A01G438400 chr7A 632549644 632552114 2470 True 4564.000 4564 100.0000 1 2471 1 chr7A.!!$R4 2470
1 TraesCS7A01G438400 chr7A 632526569 632527449 880 False 1206.000 1206 91.3530 938 1830 1 chr7A.!!$F3 892
2 TraesCS7A01G438400 chr7A 632531889 632532689 800 False 1123.000 1123 92.2980 784 1570 1 chr7A.!!$F4 786
3 TraesCS7A01G438400 chr7A 167741835 167742602 767 True 990.000 990 90.4390 1 748 1 chr7A.!!$R2 747
4 TraesCS7A01G438400 chr7A 85186386 85187022 636 True 619.000 619 85.0930 140 748 1 chr7A.!!$R1 608
5 TraesCS7A01G438400 chr7B 592347522 592348607 1085 True 1369.000 1369 89.2670 746 1861 1 chr7B.!!$R2 1115
6 TraesCS7A01G438400 chr7B 591723711 591724439 728 False 992.000 992 91.6320 784 1495 1 chr7B.!!$F3 711
7 TraesCS7A01G438400 chr7B 591713253 591714051 798 False 839.000 839 86.3860 802 1570 1 chr7B.!!$F2 768
8 TraesCS7A01G438400 chr7B 591949318 591950606 1288 False 769.000 1395 94.7730 795 2047 2 chr7B.!!$F5 1252
9 TraesCS7A01G438400 chr7B 592354606 592355554 948 True 647.500 1027 87.9955 784 1831 2 chr7B.!!$R4 1047
10 TraesCS7A01G438400 chr7B 624354612 624355232 620 True 579.000 579 84.0190 140 750 1 chr7B.!!$R3 610
11 TraesCS7A01G438400 chr7D 548708853 548709572 719 False 913.000 913 90.0140 796 1495 1 chr7D.!!$F2 699
12 TraesCS7A01G438400 chr7D 548696962 548697667 705 False 839.000 839 88.5470 802 1495 1 chr7D.!!$F1 693
13 TraesCS7A01G438400 chr7D 548781373 548782243 870 True 568.500 1007 86.4300 780 1751 2 chr7D.!!$R2 971
14 TraesCS7A01G438400 chr7D 548774892 548776824 1932 True 408.925 1258 90.9405 781 2471 4 chr7D.!!$R1 1690
15 TraesCS7A01G438400 chr2A 158032883 158033636 753 False 1007.000 1007 91.0530 1 744 1 chr2A.!!$F2 743
16 TraesCS7A01G438400 chr2A 713228725 713229300 575 True 702.000 702 89.3100 188 744 1 chr2A.!!$R2 556
17 TraesCS7A01G438400 chr2A 746929972 746930601 629 False 616.000 616 85.1740 147 747 1 chr2A.!!$F3 600
18 TraesCS7A01G438400 chr1A 42196414 42197164 750 True 1007.000 1007 91.2300 1 742 1 chr1A.!!$R2 741
19 TraesCS7A01G438400 chr1A 41372533 41373273 740 True 942.000 942 89.8680 1 742 1 chr1A.!!$R1 741
20 TraesCS7A01G438400 chr1A 451855251 451855875 624 True 573.000 573 84.1120 140 746 1 chr1A.!!$R3 606
21 TraesCS7A01G438400 chr5A 568620702 568621472 770 True 1000.000 1000 90.6740 1 744 1 chr5A.!!$R3 743
22 TraesCS7A01G438400 chr5A 566617857 566618608 751 False 994.000 994 90.8140 1 744 1 chr5A.!!$F2 743
23 TraesCS7A01G438400 chr5A 467368093 467368854 761 True 926.000 926 89.0770 1 744 1 chr5A.!!$R2 743
24 TraesCS7A01G438400 chr5A 561113759 561114371 612 False 676.000 676 87.1020 140 744 1 chr5A.!!$F1 604
25 TraesCS7A01G438400 chr5A 588410080 588410685 605 False 496.000 496 82.1660 147 748 1 chr5A.!!$F3 601
26 TraesCS7A01G438400 chr6A 614241093 614241852 759 False 952.000 952 89.7140 1 744 1 chr6A.!!$F1 743
27 TraesCS7A01G438400 chr3A 552466345 552467052 707 True 920.000 920 90.4630 51 747 1 chr3A.!!$R1 696
28 TraesCS7A01G438400 chr3A 704457901 704458526 625 False 579.000 579 84.3510 147 747 1 chr3A.!!$F2 600
29 TraesCS7A01G438400 chr2B 21456779 21457413 634 False 592.000 592 84.3510 140 744 1 chr2B.!!$F1 604

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
948 1118 0.676782 CCTCCGCGAAATCCCAAACT 60.677 55.0 8.23 0.0 0.0 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2447 3029 0.178533 GAGCTGCTTGATCTCTGCCT 59.821 55.0 2.53 0.0 0.0 4.75 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
205 207 4.891727 ATAGCCCGGCGCGACTTG 62.892 66.667 12.10 0.38 44.76 3.16
413 421 2.265739 GATGCAGCAGGGACGACA 59.734 61.111 0.00 0.00 0.00 4.35
751 898 1.383803 GGAGATGCCCTGAGTCCCT 60.384 63.158 0.00 0.00 0.00 4.20
754 901 0.757188 AGATGCCCTGAGTCCCTACG 60.757 60.000 0.00 0.00 0.00 3.51
778 925 6.072728 CGATCCATATCTTTATCCCGCAAAAA 60.073 38.462 0.00 0.00 0.00 1.94
902 1060 2.711009 CCATAAATACCCAGCCTCTCCA 59.289 50.000 0.00 0.00 0.00 3.86
908 1066 1.614824 CCCAGCCTCTCCACCTCTT 60.615 63.158 0.00 0.00 0.00 2.85
948 1118 0.676782 CCTCCGCGAAATCCCAAACT 60.677 55.000 8.23 0.00 0.00 2.66
956 1126 2.490509 CGAAATCCCAAACTACCAACCC 59.509 50.000 0.00 0.00 0.00 4.11
957 1127 2.209690 AATCCCAAACTACCAACCCG 57.790 50.000 0.00 0.00 0.00 5.28
1087 1265 1.296715 CCCAGGAAGAAGTCGGTGG 59.703 63.158 0.00 0.00 32.87 4.61
1496 1697 1.437735 CGCGCATCGATTAGCTTGC 60.438 57.895 8.75 8.08 41.67 4.01
1498 1699 1.202568 CGCATCGATTAGCTTGCCG 59.797 57.895 0.00 0.00 0.00 5.69
1500 1701 0.041839 GCATCGATTAGCTTGCCGTG 60.042 55.000 0.00 0.00 0.00 4.94
1502 1703 0.179073 ATCGATTAGCTTGCCGTGCT 60.179 50.000 0.00 0.00 43.79 4.40
1503 1704 0.391130 TCGATTAGCTTGCCGTGCTT 60.391 50.000 0.00 0.00 41.46 3.91
1561 1779 6.638610 TGCCAAGAAAGAACAATTCAGAAAA 58.361 32.000 0.00 0.00 0.00 2.29
1562 1780 6.534793 TGCCAAGAAAGAACAATTCAGAAAAC 59.465 34.615 0.00 0.00 0.00 2.43
1567 1785 8.980481 AGAAAGAACAATTCAGAAAACCTCTA 57.020 30.769 0.00 0.00 31.12 2.43
1577 1795 6.049955 TCAGAAAACCTCTATTCGATTGGT 57.950 37.500 0.00 0.00 31.12 3.67
1587 1805 1.365699 TTCGATTGGTTTAGCCGCTC 58.634 50.000 0.00 0.00 41.21 5.03
1651 1870 0.523072 TGCTGCGAAGAGGAAAATGC 59.477 50.000 0.00 0.00 0.00 3.56
1682 1901 6.906659 TCTCTCTGATTTGAGCAAATTGTTC 58.093 36.000 9.57 2.77 40.77 3.18
1686 1905 6.272318 TCTGATTTGAGCAAATTGTTCGTTT 58.728 32.000 9.57 0.00 40.77 3.60
1697 1922 6.678245 GCAAATTGTTCGTTTTTCTTCTGTTG 59.322 34.615 0.00 0.00 0.00 3.33
1707 1932 5.461032 TTTTCTTCTGTTGTTGGTGTTGT 57.539 34.783 0.00 0.00 0.00 3.32
1708 1935 4.433186 TTCTTCTGTTGTTGGTGTTGTG 57.567 40.909 0.00 0.00 0.00 3.33
1728 1962 3.063452 GTGATGTTAACATAGGTGCGGTG 59.937 47.826 20.83 0.00 36.57 4.94
1731 1965 0.253610 TTAACATAGGTGCGGTGGGG 59.746 55.000 0.00 0.00 0.00 4.96
1782 2017 6.867662 ACATTTCTTTCTTGTGGTACTGAG 57.132 37.500 0.00 0.00 0.00 3.35
1783 2018 5.239525 ACATTTCTTTCTTGTGGTACTGAGC 59.760 40.000 0.00 0.00 0.00 4.26
1784 2019 3.026630 TCTTTCTTGTGGTACTGAGCG 57.973 47.619 0.00 0.00 0.00 5.03
1785 2020 2.069273 CTTTCTTGTGGTACTGAGCGG 58.931 52.381 0.00 0.00 0.00 5.52
1786 2021 1.334160 TTCTTGTGGTACTGAGCGGA 58.666 50.000 0.00 0.00 0.00 5.54
1787 2022 0.888619 TCTTGTGGTACTGAGCGGAG 59.111 55.000 0.00 0.00 0.00 4.63
1788 2023 0.603569 CTTGTGGTACTGAGCGGAGT 59.396 55.000 0.00 0.00 0.00 3.85
1789 2024 1.000955 CTTGTGGTACTGAGCGGAGTT 59.999 52.381 0.00 0.00 0.00 3.01
1790 2025 0.601558 TGTGGTACTGAGCGGAGTTC 59.398 55.000 0.00 0.00 38.58 3.01
1791 2026 0.456312 GTGGTACTGAGCGGAGTTCG 60.456 60.000 0.00 0.00 42.00 3.95
1840 2086 1.486310 AGCGATGCCCAAGATGAAGTA 59.514 47.619 0.00 0.00 0.00 2.24
1842 2088 2.289002 GCGATGCCCAAGATGAAGTAAG 59.711 50.000 0.00 0.00 0.00 2.34
1850 2096 5.569428 GCCCAAGATGAAGTAAGCCAAAATT 60.569 40.000 0.00 0.00 0.00 1.82
1880 2221 1.942657 CATGTAATCGGTTGGAGCCAG 59.057 52.381 0.00 0.00 0.00 4.85
1887 2228 1.076485 GGTTGGAGCCAGCCATGAT 60.076 57.895 16.43 0.00 45.06 2.45
1904 2245 4.443457 CCATGATTCTCTGTAACGGTGGAT 60.443 45.833 0.00 0.00 0.00 3.41
1912 2253 3.119137 TCTGTAACGGTGGATGATGACAG 60.119 47.826 0.00 0.00 35.48 3.51
1914 2255 3.764972 TGTAACGGTGGATGATGACAGTA 59.235 43.478 0.00 0.00 0.00 2.74
1925 2266 4.492494 TGATGACAGTACCATCAGCAAT 57.508 40.909 11.36 0.00 43.67 3.56
1926 2267 4.193865 TGATGACAGTACCATCAGCAATG 58.806 43.478 11.36 0.00 43.67 2.82
1927 2268 2.358957 TGACAGTACCATCAGCAATGC 58.641 47.619 0.00 0.00 33.71 3.56
1928 2269 2.026915 TGACAGTACCATCAGCAATGCT 60.027 45.455 0.00 0.00 40.77 3.79
1929 2270 3.197549 TGACAGTACCATCAGCAATGCTA 59.802 43.478 7.70 0.00 36.40 3.49
1940 2295 1.020437 GCAATGCTAGAGCTTGGTCC 58.980 55.000 0.00 0.00 42.66 4.46
1955 2310 3.025322 TGGTCCCAAGCTGAAAAGAAA 57.975 42.857 0.00 0.00 0.00 2.52
1957 2312 3.384467 TGGTCCCAAGCTGAAAAGAAAAG 59.616 43.478 0.00 0.00 0.00 2.27
1958 2313 3.636764 GGTCCCAAGCTGAAAAGAAAAGA 59.363 43.478 0.00 0.00 0.00 2.52
1959 2314 4.099419 GGTCCCAAGCTGAAAAGAAAAGAA 59.901 41.667 0.00 0.00 0.00 2.52
1960 2315 5.043903 GTCCCAAGCTGAAAAGAAAAGAAC 58.956 41.667 0.00 0.00 0.00 3.01
1961 2316 4.956075 TCCCAAGCTGAAAAGAAAAGAACT 59.044 37.500 0.00 0.00 0.00 3.01
1962 2317 6.039382 GTCCCAAGCTGAAAAGAAAAGAACTA 59.961 38.462 0.00 0.00 0.00 2.24
1963 2318 6.263168 TCCCAAGCTGAAAAGAAAAGAACTAG 59.737 38.462 0.00 0.00 0.00 2.57
2128 2523 6.201425 CAGCTCAAACAAATTATGTGCAAACT 59.799 34.615 0.00 0.00 42.99 2.66
2129 2524 6.201425 AGCTCAAACAAATTATGTGCAAACTG 59.799 34.615 0.00 0.00 42.99 3.16
2131 2526 6.577103 TCAAACAAATTATGTGCAAACTGGA 58.423 32.000 0.00 0.00 42.99 3.86
2137 2532 5.734855 ATTATGTGCAAACTGGACGATAC 57.265 39.130 0.00 0.00 41.94 2.24
2148 2543 7.593644 GCAAACTGGACGATACTTGTTAAATTT 59.406 33.333 0.00 0.00 0.00 1.82
2179 2574 2.433662 ACCTACTACTCCCTCCGTTC 57.566 55.000 0.00 0.00 0.00 3.95
2181 2576 2.299521 CCTACTACTCCCTCCGTTCTG 58.700 57.143 0.00 0.00 0.00 3.02
2183 2578 2.830651 ACTACTCCCTCCGTTCTGAT 57.169 50.000 0.00 0.00 0.00 2.90
2185 2580 3.442076 ACTACTCCCTCCGTTCTGATTT 58.558 45.455 0.00 0.00 0.00 2.17
2186 2581 4.607239 ACTACTCCCTCCGTTCTGATTTA 58.393 43.478 0.00 0.00 0.00 1.40
2187 2582 3.889520 ACTCCCTCCGTTCTGATTTAC 57.110 47.619 0.00 0.00 0.00 2.01
2188 2583 3.442076 ACTCCCTCCGTTCTGATTTACT 58.558 45.455 0.00 0.00 0.00 2.24
2192 2587 3.933332 CCCTCCGTTCTGATTTACTTGTC 59.067 47.826 0.00 0.00 0.00 3.18
2193 2588 4.562757 CCCTCCGTTCTGATTTACTTGTCA 60.563 45.833 0.00 0.00 0.00 3.58
2195 2590 5.643777 CCTCCGTTCTGATTTACTTGTCAAT 59.356 40.000 0.00 0.00 0.00 2.57
2196 2591 6.402550 CCTCCGTTCTGATTTACTTGTCAATG 60.403 42.308 0.00 0.00 0.00 2.82
2197 2592 5.411361 TCCGTTCTGATTTACTTGTCAATGG 59.589 40.000 0.00 0.00 0.00 3.16
2198 2593 5.181245 CCGTTCTGATTTACTTGTCAATGGT 59.819 40.000 0.00 0.00 0.00 3.55
2199 2594 6.293955 CCGTTCTGATTTACTTGTCAATGGTT 60.294 38.462 0.00 0.00 0.00 3.67
2201 2596 7.647715 CGTTCTGATTTACTTGTCAATGGTTTT 59.352 33.333 0.00 0.00 0.00 2.43
2202 2597 9.959749 GTTCTGATTTACTTGTCAATGGTTTTA 57.040 29.630 0.00 0.00 0.00 1.52
2207 2602 9.959749 GATTTACTTGTCAATGGTTTTAGTTCA 57.040 29.630 0.00 0.00 0.00 3.18
2212 2607 9.665719 ACTTGTCAATGGTTTTAGTTCAAATTT 57.334 25.926 0.00 0.00 0.00 1.82
2213 2608 9.919348 CTTGTCAATGGTTTTAGTTCAAATTTG 57.081 29.630 12.15 12.15 0.00 2.32
2214 2609 9.658799 TTGTCAATGGTTTTAGTTCAAATTTGA 57.341 25.926 16.91 16.91 34.92 2.69
2229 2624 6.367421 TCAAATTTGAACTAAATCCACGACG 58.633 36.000 18.45 0.00 38.01 5.12
2231 2626 5.779806 ATTTGAACTAAATCCACGACGAG 57.220 39.130 0.00 0.00 33.79 4.18
2233 2628 5.375417 TTGAACTAAATCCACGACGAGTA 57.625 39.130 0.00 0.00 0.00 2.59
2234 2629 5.375417 TGAACTAAATCCACGACGAGTAA 57.625 39.130 0.00 0.00 0.00 2.24
2235 2630 5.771469 TGAACTAAATCCACGACGAGTAAA 58.229 37.500 0.00 0.00 0.00 2.01
2236 2631 6.392354 TGAACTAAATCCACGACGAGTAAAT 58.608 36.000 0.00 0.00 0.00 1.40
2237 2632 6.529125 TGAACTAAATCCACGACGAGTAAATC 59.471 38.462 0.00 0.00 0.00 2.17
2260 2655 4.723309 GGAACGGAGGGAGTACTAGATTA 58.277 47.826 0.00 0.00 0.00 1.75
2268 2663 6.936335 GGAGGGAGTACTAGATTACTCAGTAC 59.064 46.154 17.65 11.46 46.84 2.73
2270 2665 7.870027 AGGGAGTACTAGATTACTCAGTACAA 58.130 38.462 17.65 0.00 46.84 2.41
2271 2666 8.334734 AGGGAGTACTAGATTACTCAGTACAAA 58.665 37.037 17.65 0.00 46.84 2.83
2272 2667 8.623030 GGGAGTACTAGATTACTCAGTACAAAG 58.377 40.741 17.65 0.00 46.84 2.77
2273 2668 9.176460 GGAGTACTAGATTACTCAGTACAAAGT 57.824 37.037 17.65 0.20 46.84 2.66
2274 2669 9.991388 GAGTACTAGATTACTCAGTACAAAGTG 57.009 37.037 13.16 0.00 45.12 3.16
2275 2670 9.517868 AGTACTAGATTACTCAGTACAAAGTGT 57.482 33.333 17.09 2.70 44.57 3.55
2276 2671 9.557338 GTACTAGATTACTCAGTACAAAGTGTG 57.443 37.037 9.68 0.00 42.65 3.82
2277 2672 8.179509 ACTAGATTACTCAGTACAAAGTGTGT 57.820 34.615 9.68 0.00 44.82 3.72
2278 2673 8.082852 ACTAGATTACTCAGTACAAAGTGTGTG 58.917 37.037 9.68 0.00 41.89 3.82
2279 2674 6.817184 AGATTACTCAGTACAAAGTGTGTGT 58.183 36.000 9.68 1.61 41.89 3.72
2280 2675 6.701841 AGATTACTCAGTACAAAGTGTGTGTG 59.298 38.462 9.68 0.00 41.89 3.82
2281 2676 4.202245 ACTCAGTACAAAGTGTGTGTGT 57.798 40.909 0.00 0.00 41.89 3.72
2313 2708 5.305386 TGTGTTGAGCTAGCTATGGATGTAT 59.695 40.000 19.38 0.00 0.00 2.29
2323 2718 9.535878 GCTAGCTATGGATGTATTATTACCTTC 57.464 37.037 7.70 0.00 0.00 3.46
2337 2770 5.757850 ATTACCTTCGCAATTCCAGATTC 57.242 39.130 0.00 0.00 0.00 2.52
2347 2781 2.795231 TTCCAGATTCCCAGCTCTTG 57.205 50.000 0.00 0.00 0.00 3.02
2365 2799 4.279145 TCTTGGTGACCTCCATAGTACTC 58.721 47.826 2.11 0.00 37.33 2.59
2366 2800 3.028094 TGGTGACCTCCATAGTACTCC 57.972 52.381 2.11 0.00 31.96 3.85
2367 2801 2.313643 TGGTGACCTCCATAGTACTCCA 59.686 50.000 2.11 0.00 31.96 3.86
2368 2802 3.245839 TGGTGACCTCCATAGTACTCCAA 60.246 47.826 2.11 0.00 31.96 3.53
2427 2993 1.133513 TCTGTTTTGGCAGGGTGATGT 60.134 47.619 0.00 0.00 37.12 3.06
2447 3029 2.596851 GGCTGTGGCTGGAGAGGAA 61.597 63.158 0.00 0.00 38.73 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
137 138 3.382832 CTTGGGCTCGACGAGGGT 61.383 66.667 25.31 0.00 0.00 4.34
310 312 1.970114 GACACCGTCCTCGTCCTCA 60.970 63.158 0.00 0.00 35.01 3.86
445 462 0.868602 CACCGTTGTCGTCGTTGTCT 60.869 55.000 0.00 0.00 35.01 3.41
609 716 8.061268 CACGGGTTTTAAAATGTTCAAATTCTG 58.939 33.333 3.52 0.00 0.00 3.02
610 717 7.225734 CCACGGGTTTTAAAATGTTCAAATTCT 59.774 33.333 3.52 0.00 0.00 2.40
751 898 4.707934 TGCGGGATAAAGATATGGATCGTA 59.292 41.667 0.00 0.00 37.15 3.43
754 901 6.817765 TTTTGCGGGATAAAGATATGGATC 57.182 37.500 0.00 0.00 0.00 3.36
778 925 7.012421 GTCCTCTGCGTAAAGATATGGAATTTT 59.988 37.037 0.00 0.00 0.00 1.82
781 928 5.070446 TGTCCTCTGCGTAAAGATATGGAAT 59.930 40.000 0.00 0.00 0.00 3.01
782 929 4.404394 TGTCCTCTGCGTAAAGATATGGAA 59.596 41.667 0.00 0.00 0.00 3.53
840 987 2.960129 CGCGTGCTCGGGTATTCC 60.960 66.667 16.03 0.00 43.36 3.01
882 1029 3.496870 GGTGGAGAGGCTGGGTATTTATG 60.497 52.174 0.00 0.00 0.00 1.90
883 1041 2.711547 GGTGGAGAGGCTGGGTATTTAT 59.288 50.000 0.00 0.00 0.00 1.40
902 1060 1.075659 GCTGCTGGGGAAAAGAGGT 59.924 57.895 0.00 0.00 0.00 3.85
908 1066 3.171828 TTCGTCGCTGCTGGGGAAA 62.172 57.895 7.80 0.00 38.62 3.13
948 1118 0.398098 GAGGAGGGATCGGGTTGGTA 60.398 60.000 0.00 0.00 0.00 3.25
956 1126 2.203714 GAGGGGGAGGAGGGATCG 60.204 72.222 0.00 0.00 0.00 3.69
957 1127 2.203714 CGAGGGGGAGGAGGGATC 60.204 72.222 0.00 0.00 0.00 3.36
1467 1654 1.081509 GATGCGCGCCTCTCTCTAG 60.082 63.158 30.77 0.00 0.00 2.43
1496 1697 4.000988 ACCATTAGTTCTACAAAGCACGG 58.999 43.478 0.00 0.00 0.00 4.94
1498 1699 6.073440 TCGAAACCATTAGTTCTACAAAGCAC 60.073 38.462 0.00 0.00 37.88 4.40
1500 1701 6.476243 TCGAAACCATTAGTTCTACAAAGC 57.524 37.500 0.00 0.00 37.88 3.51
1502 1703 7.972832 ACATCGAAACCATTAGTTCTACAAA 57.027 32.000 0.00 0.00 37.88 2.83
1503 1704 8.525316 TCTACATCGAAACCATTAGTTCTACAA 58.475 33.333 0.00 0.00 37.88 2.41
1561 1779 4.704965 GGCTAAACCAATCGAATAGAGGT 58.295 43.478 0.00 0.00 38.86 3.85
1562 1780 3.741344 CGGCTAAACCAATCGAATAGAGG 59.259 47.826 0.00 0.00 39.03 3.69
1567 1785 1.940613 GAGCGGCTAAACCAATCGAAT 59.059 47.619 0.60 0.00 39.03 3.34
1577 1795 1.135139 CAGAGCACTAGAGCGGCTAAA 59.865 52.381 0.60 0.00 38.15 1.85
1682 1901 4.481463 ACACCAACAACAGAAGAAAAACG 58.519 39.130 0.00 0.00 0.00 3.60
1686 1905 4.520874 TCACAACACCAACAACAGAAGAAA 59.479 37.500 0.00 0.00 0.00 2.52
1697 1922 6.016610 ACCTATGTTAACATCACAACACCAAC 60.017 38.462 24.00 0.00 37.47 3.77
1707 1932 3.266636 CACCGCACCTATGTTAACATCA 58.733 45.455 24.00 10.24 37.76 3.07
1708 1935 2.612212 CCACCGCACCTATGTTAACATC 59.388 50.000 24.00 9.03 37.76 3.06
1728 1962 3.003480 CGAACAGATCTGAGTTTTCCCC 58.997 50.000 29.27 1.27 0.00 4.81
1731 1965 7.355778 ACAAATTCGAACAGATCTGAGTTTTC 58.644 34.615 29.27 19.29 0.00 2.29
1783 2018 0.179134 CTCCACTAAGGCGAACTCCG 60.179 60.000 0.00 0.00 42.21 4.63
1784 2019 0.896226 ACTCCACTAAGGCGAACTCC 59.104 55.000 0.00 0.00 37.29 3.85
1785 2020 2.231721 AGAACTCCACTAAGGCGAACTC 59.768 50.000 0.00 0.00 37.29 3.01
1786 2021 2.231721 GAGAACTCCACTAAGGCGAACT 59.768 50.000 0.00 0.00 37.29 3.01
1787 2022 2.608268 GAGAACTCCACTAAGGCGAAC 58.392 52.381 0.00 0.00 37.29 3.95
1840 2086 7.472334 ACATGATCTCAACTAATTTTGGCTT 57.528 32.000 0.00 0.00 0.00 4.35
1842 2088 9.455847 GATTACATGATCTCAACTAATTTTGGC 57.544 33.333 0.00 0.00 0.00 4.52
1850 2096 6.097696 TCCAACCGATTACATGATCTCAACTA 59.902 38.462 0.00 0.00 0.00 2.24
1880 2221 2.609459 CACCGTTACAGAGAATCATGGC 59.391 50.000 0.00 0.00 37.82 4.40
1887 2228 3.767131 TCATCATCCACCGTTACAGAGAA 59.233 43.478 0.00 0.00 0.00 2.87
1904 2245 3.979101 TTGCTGATGGTACTGTCATCA 57.021 42.857 11.34 11.34 45.86 3.07
1912 2253 2.805099 GCTCTAGCATTGCTGATGGTAC 59.195 50.000 21.31 0.79 44.30 3.34
1923 2264 1.289160 TGGGACCAAGCTCTAGCATT 58.711 50.000 4.54 0.00 45.16 3.56
1925 2266 0.615331 CTTGGGACCAAGCTCTAGCA 59.385 55.000 17.34 0.00 45.38 3.49
1926 2267 3.467776 CTTGGGACCAAGCTCTAGC 57.532 57.895 17.34 0.00 45.38 3.42
1940 2295 6.263168 TCCTAGTTCTTTTCTTTTCAGCTTGG 59.737 38.462 0.00 0.00 0.00 3.61
1955 2310 1.657804 CTGGGGGTGTCCTAGTTCTT 58.342 55.000 0.00 0.00 39.09 2.52
1957 2312 0.252558 TCCTGGGGGTGTCCTAGTTC 60.253 60.000 0.00 0.00 42.02 3.01
1958 2313 0.195096 TTCCTGGGGGTGTCCTAGTT 59.805 55.000 0.00 0.00 42.02 2.24
1959 2314 0.546988 GTTCCTGGGGGTGTCCTAGT 60.547 60.000 0.00 0.00 42.02 2.57
1960 2315 1.272554 GGTTCCTGGGGGTGTCCTAG 61.273 65.000 0.00 0.00 43.09 3.02
1961 2316 1.229723 GGTTCCTGGGGGTGTCCTA 60.230 63.158 0.00 0.00 35.33 2.94
1962 2317 2.531942 GGTTCCTGGGGGTGTCCT 60.532 66.667 0.00 0.00 35.33 3.85
1963 2318 2.211468 GATGGTTCCTGGGGGTGTCC 62.211 65.000 0.00 0.00 0.00 4.02
2128 2523 7.655236 TTCGAAATTTAACAAGTATCGTCCA 57.345 32.000 0.00 0.00 0.00 4.02
2148 2543 8.773033 AGGGAGTAGTAGGTAAAATATTTCGA 57.227 34.615 0.10 0.00 0.00 3.71
2170 2565 3.933332 GACAAGTAAATCAGAACGGAGGG 59.067 47.826 0.00 0.00 0.00 4.30
2179 2574 9.965824 AACTAAAACCATTGACAAGTAAATCAG 57.034 29.630 0.00 0.00 0.00 2.90
2181 2576 9.959749 TGAACTAAAACCATTGACAAGTAAATC 57.040 29.630 0.00 0.00 0.00 2.17
2186 2581 9.665719 AAATTTGAACTAAAACCATTGACAAGT 57.334 25.926 0.00 0.00 0.00 3.16
2187 2582 9.919348 CAAATTTGAACTAAAACCATTGACAAG 57.081 29.630 13.08 0.00 0.00 3.16
2188 2583 9.658799 TCAAATTTGAACTAAAACCATTGACAA 57.341 25.926 18.45 0.00 33.55 3.18
2207 2602 6.204108 ACTCGTCGTGGATTTAGTTCAAATTT 59.796 34.615 0.00 0.00 36.96 1.82
2208 2603 5.699458 ACTCGTCGTGGATTTAGTTCAAATT 59.301 36.000 0.00 0.00 36.96 1.82
2210 2605 4.624015 ACTCGTCGTGGATTTAGTTCAAA 58.376 39.130 0.00 0.00 0.00 2.69
2212 2607 3.928727 ACTCGTCGTGGATTTAGTTCA 57.071 42.857 0.00 0.00 0.00 3.18
2213 2608 6.290956 CGATTTACTCGTCGTGGATTTAGTTC 60.291 42.308 0.00 0.00 42.56 3.01
2214 2609 5.514204 CGATTTACTCGTCGTGGATTTAGTT 59.486 40.000 0.00 0.00 42.56 2.24
2216 2611 4.440103 CCGATTTACTCGTCGTGGATTTAG 59.560 45.833 0.00 0.00 46.18 1.85
2217 2612 4.096231 TCCGATTTACTCGTCGTGGATTTA 59.904 41.667 0.00 0.00 46.18 1.40
2218 2613 3.119388 TCCGATTTACTCGTCGTGGATTT 60.119 43.478 0.00 0.00 46.18 2.17
2219 2614 2.424601 TCCGATTTACTCGTCGTGGATT 59.575 45.455 0.00 0.00 46.18 3.01
2220 2615 2.019249 TCCGATTTACTCGTCGTGGAT 58.981 47.619 0.00 0.00 46.18 3.41
2221 2616 1.452110 TCCGATTTACTCGTCGTGGA 58.548 50.000 0.00 0.00 46.18 4.02
2222 2617 1.916000 GTTCCGATTTACTCGTCGTGG 59.084 52.381 0.00 0.00 46.18 4.94
2223 2618 1.576246 CGTTCCGATTTACTCGTCGTG 59.424 52.381 0.00 0.00 46.18 4.35
2226 2621 2.448219 CTCCGTTCCGATTTACTCGTC 58.552 52.381 0.00 0.00 46.18 4.20
2227 2622 1.133790 CCTCCGTTCCGATTTACTCGT 59.866 52.381 0.00 0.00 46.18 4.18
2229 2624 1.753073 TCCCTCCGTTCCGATTTACTC 59.247 52.381 0.00 0.00 0.00 2.59
2231 2626 1.479730 ACTCCCTCCGTTCCGATTTAC 59.520 52.381 0.00 0.00 0.00 2.01
2233 2628 1.479730 GTACTCCCTCCGTTCCGATTT 59.520 52.381 0.00 0.00 0.00 2.17
2234 2629 1.109609 GTACTCCCTCCGTTCCGATT 58.890 55.000 0.00 0.00 0.00 3.34
2235 2630 0.258194 AGTACTCCCTCCGTTCCGAT 59.742 55.000 0.00 0.00 0.00 4.18
2236 2631 0.911769 TAGTACTCCCTCCGTTCCGA 59.088 55.000 0.00 0.00 0.00 4.55
2237 2632 1.134280 TCTAGTACTCCCTCCGTTCCG 60.134 57.143 0.00 0.00 0.00 4.30
2238 2633 2.725221 TCTAGTACTCCCTCCGTTCC 57.275 55.000 0.00 0.00 0.00 3.62
2239 2634 5.375773 AGTAATCTAGTACTCCCTCCGTTC 58.624 45.833 0.00 0.00 27.56 3.95
2240 2635 5.104193 TGAGTAATCTAGTACTCCCTCCGTT 60.104 44.000 14.68 0.00 46.39 4.44
2241 2636 4.411540 TGAGTAATCTAGTACTCCCTCCGT 59.588 45.833 14.68 0.00 46.39 4.69
2242 2637 4.970711 TGAGTAATCTAGTACTCCCTCCG 58.029 47.826 14.68 0.00 46.39 4.63
2243 2638 5.944135 ACTGAGTAATCTAGTACTCCCTCC 58.056 45.833 14.68 0.00 46.39 4.30
2244 2639 7.507829 TGTACTGAGTAATCTAGTACTCCCTC 58.492 42.308 21.92 0.00 46.39 4.30
2245 2640 7.448915 TGTACTGAGTAATCTAGTACTCCCT 57.551 40.000 21.92 5.63 46.39 4.20
2246 2641 8.517062 TTTGTACTGAGTAATCTAGTACTCCC 57.483 38.462 21.92 7.34 46.39 4.30
2247 2642 9.176460 ACTTTGTACTGAGTAATCTAGTACTCC 57.824 37.037 21.92 3.96 46.39 3.85
2260 2655 3.932710 CACACACACACTTTGTACTGAGT 59.067 43.478 0.00 0.00 35.67 3.41
2268 2663 2.031245 ACACACACACACACACACTTTG 60.031 45.455 0.00 0.00 0.00 2.77
2270 2665 1.535028 CACACACACACACACACACTT 59.465 47.619 0.00 0.00 0.00 3.16
2271 2666 1.155889 CACACACACACACACACACT 58.844 50.000 0.00 0.00 0.00 3.55
2272 2667 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2273 2668 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2274 2669 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2275 2670 1.265365 CAACACACACACACACACACA 59.735 47.619 0.00 0.00 0.00 3.72
2276 2671 1.533299 TCAACACACACACACACACAC 59.467 47.619 0.00 0.00 0.00 3.82
2277 2672 1.803555 CTCAACACACACACACACACA 59.196 47.619 0.00 0.00 0.00 3.72
2278 2673 1.465689 GCTCAACACACACACACACAC 60.466 52.381 0.00 0.00 0.00 3.82
2279 2674 0.801872 GCTCAACACACACACACACA 59.198 50.000 0.00 0.00 0.00 3.72
2280 2675 1.086696 AGCTCAACACACACACACAC 58.913 50.000 0.00 0.00 0.00 3.82
2281 2676 2.549926 CTAGCTCAACACACACACACA 58.450 47.619 0.00 0.00 0.00 3.72
2313 2708 6.262273 GGAATCTGGAATTGCGAAGGTAATAA 59.738 38.462 0.00 0.00 0.00 1.40
2323 2718 0.383231 GCTGGGAATCTGGAATTGCG 59.617 55.000 0.00 0.00 0.00 4.85
2347 2781 3.028094 TGGAGTACTATGGAGGTCACC 57.972 52.381 0.00 0.00 0.00 4.02
2365 2799 0.179129 GGGTGAAAGCGCATCATTGG 60.179 55.000 17.28 0.00 33.03 3.16
2366 2800 0.813184 AGGGTGAAAGCGCATCATTG 59.187 50.000 17.28 0.00 33.03 2.82
2367 2801 1.549203 AAGGGTGAAAGCGCATCATT 58.451 45.000 17.28 6.89 33.03 2.57
2368 2802 1.474077 GAAAGGGTGAAAGCGCATCAT 59.526 47.619 17.28 3.06 33.03 2.45
2402 2968 2.231235 CACCCTGCCAAAACAGATAACC 59.769 50.000 0.00 0.00 40.25 2.85
2427 2993 2.752358 CTCTCCAGCCACAGCCAA 59.248 61.111 0.00 0.00 41.25 4.52
2447 3029 0.178533 GAGCTGCTTGATCTCTGCCT 59.821 55.000 2.53 0.00 0.00 4.75


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

AutoCloner maintained by Alex Coulton.