Multiple sequence alignment - TraesCS2D01G597400

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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 TraesCS2D01G597400 chr2D 100.000 2258 0 0 1 2258 649813410 649811153 0.000000e+00 4170.0
1 TraesCS2D01G597400 chr2D 80.368 163 23 7 1762 1923 315193820 315193666 5.100000e-22 115.0
2 TraesCS2D01G597400 chr2D 80.255 157 21 6 1769 1923 634467738 634467886 2.370000e-20 110.0
3 TraesCS2D01G597400 chr2D 85.915 71 9 1 1854 1923 63902860 63902790 8.650000e-10 75.0
4 TraesCS2D01G597400 chr2B 85.240 813 54 36 652 1452 785885751 785884993 0.000000e+00 776.0
5 TraesCS2D01G597400 chr2B 85.468 695 47 25 1587 2258 785884988 785884325 0.000000e+00 675.0
6 TraesCS2D01G597400 chr2B 91.610 441 29 5 3 436 785886463 785886024 8.920000e-169 603.0
7 TraesCS2D01G597400 chr2B 89.583 192 14 3 435 620 785885942 785885751 2.900000e-59 239.0
8 TraesCS2D01G597400 chr2B 81.098 164 21 6 1762 1923 777441801 777441956 3.050000e-24 122.0
9 TraesCS2D01G597400 chr2B 100.000 29 0 0 1951 1979 485269577 485269605 1.000000e-03 54.7
10 TraesCS2D01G597400 chr2A 83.297 922 70 28 1356 2258 775022176 775023032 0.000000e+00 773.0
11 TraesCS2D01G597400 chr2A 83.616 708 47 35 652 1355 775021477 775022119 3.210000e-168 601.0
12 TraesCS2D01G597400 chr2A 91.344 439 30 5 3 435 775020782 775021218 5.370000e-166 593.0
13 TraesCS2D01G597400 chr2A 90.640 203 11 6 423 620 775021278 775021477 1.720000e-66 263.0
14 TraesCS2D01G597400 chr2A 85.345 116 16 1 1977 2092 706266761 706266647 3.940000e-23 119.0
15 TraesCS2D01G597400 chr2A 80.667 150 17 8 1773 1921 578773258 578773120 3.070000e-19 106.0
16 TraesCS2D01G597400 chr1A 87.069 116 15 0 1977 2092 552458940 552459055 5.060000e-27 132.0
17 TraesCS2D01G597400 chr7B 97.059 68 2 0 2023 2090 673670945 673670878 5.100000e-22 115.0
18 TraesCS2D01G597400 chr7B 79.085 153 25 5 1771 1923 596668333 596668188 5.130000e-17 99.0
19 TraesCS2D01G597400 chr6D 85.455 110 16 0 1983 2092 3182980 3182871 5.100000e-22 115.0
20 TraesCS2D01G597400 chr6D 83.505 97 16 0 2000 2096 472366756 472366852 8.590000e-15 91.6
21 TraesCS2D01G597400 chr5B 81.897 116 21 0 1977 2092 701201310 701201425 5.130000e-17 99.0
22 TraesCS2D01G597400 chr5B 100.000 28 0 0 1951 1978 110464726 110464699 4.000000e-03 52.8
23 TraesCS2D01G597400 chr6B 83.505 97 16 0 2000 2096 717080058 717080154 8.590000e-15 91.6
24 TraesCS2D01G597400 chr3D 87.838 74 8 1 1852 1924 600837526 600837453 4.000000e-13 86.1
25 TraesCS2D01G597400 chr5D 76.923 156 25 7 1771 1923 538647004 538646857 6.690000e-11 78.7
26 TraesCS2D01G597400 chr4B 100.000 29 0 0 1895 1923 149040764 149040792 1.000000e-03 54.7


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 TraesCS2D01G597400 chr2D 649811153 649813410 2257 True 4170.00 4170 100.00000 1 2258 1 chr2D.!!$R3 2257
1 TraesCS2D01G597400 chr2B 785884325 785886463 2138 True 573.25 776 87.97525 3 2258 4 chr2B.!!$R1 2255
2 TraesCS2D01G597400 chr2A 775020782 775023032 2250 False 557.50 773 87.22425 3 2258 4 chr2A.!!$F1 2255

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
897 1004 0.32483 CGTCTCTTCCTCCCTCCCTT 60.325 60.0 0.0 0.0 0.0 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1889 2120 0.106268 TGTTGCATGAGGGGTGTTGT 60.106 50.0 0.0 0.0 0.0 3.32 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
76 77 4.494484 GGCCTGGAAATATGTTTGTTCAC 58.506 43.478 0.00 0.00 0.00 3.18
84 86 0.667993 ATGTTTGTTCACACAGGGCG 59.332 50.000 0.00 0.00 33.22 6.13
87 89 1.444119 TTTGTTCACACAGGGCGAGC 61.444 55.000 0.00 0.00 33.22 5.03
91 93 3.357079 CACACAGGGCGAGCAACC 61.357 66.667 0.00 0.00 0.00 3.77
152 156 7.990917 TCCTTTTTGTTTTAATTTCCTTTGGC 58.009 30.769 0.00 0.00 0.00 4.52
199 203 4.383770 GGGATTGTAACTGGGATCGAGAAA 60.384 45.833 0.00 0.00 0.00 2.52
421 434 7.576236 CACAAGCCTAAATATCATTTACTCCG 58.424 38.462 0.00 0.00 0.00 4.63
424 437 7.304497 AGCCTAAATATCATTTACTCCGTCT 57.696 36.000 0.00 0.00 0.00 4.18
487 583 2.223021 CCGTTGTGAAGTGTCAACTGTG 60.223 50.000 0.00 0.00 40.88 3.66
561 664 7.013942 ACACATAGCGGTACATGTATTTCTCTA 59.986 37.037 9.18 7.28 33.66 2.43
595 698 7.771183 TGTTTTCAGTGCTCTGTTTTATTTCT 58.229 30.769 15.01 0.00 41.91 2.52
603 706 6.865205 GTGCTCTGTTTTATTTCTGCATTTCT 59.135 34.615 0.00 0.00 0.00 2.52
604 707 6.864685 TGCTCTGTTTTATTTCTGCATTTCTG 59.135 34.615 0.00 0.00 0.00 3.02
620 723 7.946207 TGCATTTCTGTTTTATCCACTTGTTA 58.054 30.769 0.00 0.00 0.00 2.41
621 724 8.081633 TGCATTTCTGTTTTATCCACTTGTTAG 58.918 33.333 0.00 0.00 0.00 2.34
622 725 8.296713 GCATTTCTGTTTTATCCACTTGTTAGA 58.703 33.333 0.00 0.00 0.00 2.10
623 726 9.612620 CATTTCTGTTTTATCCACTTGTTAGAC 57.387 33.333 0.00 0.00 0.00 2.59
624 727 8.740123 TTTCTGTTTTATCCACTTGTTAGACA 57.260 30.769 0.00 0.00 0.00 3.41
625 728 7.962964 TCTGTTTTATCCACTTGTTAGACAG 57.037 36.000 0.00 0.00 33.85 3.51
626 729 7.506114 TCTGTTTTATCCACTTGTTAGACAGT 58.494 34.615 0.00 0.00 34.14 3.55
627 730 7.990886 TCTGTTTTATCCACTTGTTAGACAGTT 59.009 33.333 0.00 0.00 34.14 3.16
628 731 9.268268 CTGTTTTATCCACTTGTTAGACAGTTA 57.732 33.333 0.00 0.00 0.00 2.24
629 732 9.787435 TGTTTTATCCACTTGTTAGACAGTTAT 57.213 29.630 0.00 0.00 0.00 1.89
635 738 8.827177 TCCACTTGTTAGACAGTTATAAACAG 57.173 34.615 0.00 0.00 32.18 3.16
636 739 8.644216 TCCACTTGTTAGACAGTTATAAACAGA 58.356 33.333 0.00 0.00 32.18 3.41
637 740 8.709646 CCACTTGTTAGACAGTTATAAACAGAC 58.290 37.037 0.00 0.00 32.18 3.51
638 741 8.709646 CACTTGTTAGACAGTTATAAACAGACC 58.290 37.037 0.00 0.00 32.18 3.85
639 742 7.876582 ACTTGTTAGACAGTTATAAACAGACCC 59.123 37.037 0.00 0.00 32.18 4.46
640 743 7.549147 TGTTAGACAGTTATAAACAGACCCT 57.451 36.000 0.00 0.00 0.00 4.34
641 744 7.970102 TGTTAGACAGTTATAAACAGACCCTT 58.030 34.615 0.00 0.00 0.00 3.95
642 745 7.876068 TGTTAGACAGTTATAAACAGACCCTTG 59.124 37.037 0.00 0.00 0.00 3.61
643 746 6.435292 AGACAGTTATAAACAGACCCTTGT 57.565 37.500 0.00 0.00 0.00 3.16
644 747 7.549147 AGACAGTTATAAACAGACCCTTGTA 57.451 36.000 0.00 0.00 0.00 2.41
645 748 7.970102 AGACAGTTATAAACAGACCCTTGTAA 58.030 34.615 0.00 0.00 0.00 2.41
646 749 7.876582 AGACAGTTATAAACAGACCCTTGTAAC 59.123 37.037 0.00 0.00 32.39 2.50
647 750 6.938596 ACAGTTATAAACAGACCCTTGTAACC 59.061 38.462 0.00 0.00 32.54 2.85
648 751 7.166167 CAGTTATAAACAGACCCTTGTAACCT 58.834 38.462 0.00 0.00 32.54 3.50
649 752 7.664318 CAGTTATAAACAGACCCTTGTAACCTT 59.336 37.037 0.00 0.00 32.54 3.50
650 753 8.883302 AGTTATAAACAGACCCTTGTAACCTTA 58.117 33.333 0.00 0.00 32.54 2.69
651 754 9.676861 GTTATAAACAGACCCTTGTAACCTTAT 57.323 33.333 0.00 0.00 0.00 1.73
685 788 6.625873 AAGAAAAACAGCAAGGAGAAGTAG 57.374 37.500 0.00 0.00 0.00 2.57
733 836 0.988832 AGGGGAGGACGCAAACATTA 59.011 50.000 0.00 0.00 33.80 1.90
734 837 1.564348 AGGGGAGGACGCAAACATTAT 59.436 47.619 0.00 0.00 33.80 1.28
776 879 1.699634 TCAAGTGACCCCCTCTTCTTG 59.300 52.381 0.00 0.00 35.15 3.02
777 880 1.068121 AAGTGACCCCCTCTTCTTGG 58.932 55.000 0.00 0.00 0.00 3.61
778 881 0.842467 AGTGACCCCCTCTTCTTGGG 60.842 60.000 0.00 0.00 45.34 4.12
799 902 2.360475 GGCTCTTCCACCCACAGC 60.360 66.667 0.00 0.00 34.01 4.40
801 904 3.160585 CTCTTCCACCCACAGCCA 58.839 61.111 0.00 0.00 0.00 4.75
803 906 2.055689 CTCTTCCACCCACAGCCACA 62.056 60.000 0.00 0.00 0.00 4.17
804 907 1.601759 CTTCCACCCACAGCCACAG 60.602 63.158 0.00 0.00 0.00 3.66
821 924 1.072159 AGGGCACACAGAAGCACTC 59.928 57.895 0.00 0.00 41.53 3.51
822 925 1.227943 GGGCACACAGAAGCACTCA 60.228 57.895 0.00 0.00 0.00 3.41
823 926 1.510480 GGGCACACAGAAGCACTCAC 61.510 60.000 0.00 0.00 0.00 3.51
837 944 7.754475 CAGAAGCACTCACTATATATACAGCAG 59.246 40.741 0.00 0.00 0.00 4.24
839 946 6.013379 AGCACTCACTATATATACAGCAGGT 58.987 40.000 0.00 0.00 0.00 4.00
842 949 6.587990 CACTCACTATATATACAGCAGGTTGC 59.412 42.308 0.00 0.00 45.46 4.17
854 961 1.404583 GCAGGTTGCACCATTCATTCC 60.405 52.381 7.86 0.00 44.26 3.01
866 973 0.674581 TTCATTCCTCCGCAGCACAG 60.675 55.000 0.00 0.00 0.00 3.66
867 974 2.437359 ATTCCTCCGCAGCACAGC 60.437 61.111 0.00 0.00 0.00 4.40
868 975 2.964310 ATTCCTCCGCAGCACAGCT 61.964 57.895 0.00 0.00 40.77 4.24
869 976 2.866085 ATTCCTCCGCAGCACAGCTC 62.866 60.000 0.00 0.00 36.40 4.09
870 977 4.383861 CCTCCGCAGCACAGCTCA 62.384 66.667 0.00 0.00 36.40 4.26
875 982 3.735029 GCAGCACAGCTCAGGCAC 61.735 66.667 3.87 0.00 36.40 5.01
876 983 2.281276 CAGCACAGCTCAGGCACA 60.281 61.111 3.87 0.00 36.40 4.57
884 991 2.936912 GCTCAGGCACACCGTCTCT 61.937 63.158 0.00 0.00 42.76 3.10
887 994 1.374758 CAGGCACACCGTCTCTTCC 60.375 63.158 0.00 0.00 42.76 3.46
894 1001 1.000612 ACCGTCTCTTCCTCCCTCC 59.999 63.158 0.00 0.00 0.00 4.30
895 1002 1.758906 CCGTCTCTTCCTCCCTCCC 60.759 68.421 0.00 0.00 0.00 4.30
896 1003 1.308326 CGTCTCTTCCTCCCTCCCT 59.692 63.158 0.00 0.00 0.00 4.20
897 1004 0.324830 CGTCTCTTCCTCCCTCCCTT 60.325 60.000 0.00 0.00 0.00 3.95
898 1005 1.897647 CGTCTCTTCCTCCCTCCCTTT 60.898 57.143 0.00 0.00 0.00 3.11
922 1029 2.125673 CCCTGTTAGTGGTCGCCG 60.126 66.667 0.00 0.00 0.00 6.46
947 1054 0.981183 CAGCACCCACCTACCTAACA 59.019 55.000 0.00 0.00 0.00 2.41
948 1055 1.066143 CAGCACCCACCTACCTAACAG 60.066 57.143 0.00 0.00 0.00 3.16
949 1056 0.981943 GCACCCACCTACCTAACAGT 59.018 55.000 0.00 0.00 0.00 3.55
952 1059 2.635915 CACCCACCTACCTAACAGTGAA 59.364 50.000 0.00 0.00 31.79 3.18
954 1061 3.072038 ACCCACCTACCTAACAGTGAAAC 59.928 47.826 0.00 0.00 31.79 2.78
955 1062 3.323243 CCACCTACCTAACAGTGAAACG 58.677 50.000 0.00 0.00 45.86 3.60
956 1063 3.006110 CCACCTACCTAACAGTGAAACGA 59.994 47.826 0.00 0.00 45.86 3.85
957 1064 3.985925 CACCTACCTAACAGTGAAACGAC 59.014 47.826 0.00 0.00 45.86 4.34
959 1066 2.877043 ACCTAACAGTGAAACGACGT 57.123 45.000 0.00 0.00 45.86 4.34
960 1067 3.988379 ACCTAACAGTGAAACGACGTA 57.012 42.857 0.00 0.00 45.86 3.57
961 1068 3.893720 ACCTAACAGTGAAACGACGTAG 58.106 45.455 0.00 0.00 45.86 3.51
1059 1175 4.816984 TCCGACGAGGAGGAGGCC 62.817 72.222 0.00 0.00 45.98 5.19
1199 1315 2.962786 CGCCGACACCAACACGAA 60.963 61.111 0.00 0.00 0.00 3.85
1204 1320 3.218209 GACACCAACACGAACGCCG 62.218 63.158 0.00 0.00 45.44 6.46
1205 1321 4.659874 CACCAACACGAACGCCGC 62.660 66.667 0.00 0.00 43.32 6.53
1244 1366 1.152777 CCAACACCAACAGGCAGGA 60.153 57.895 0.00 0.00 0.00 3.86
1246 1368 0.751277 CAACACCAACAGGCAGGACA 60.751 55.000 0.00 0.00 0.00 4.02
1271 1393 3.795041 CTAGCCTGCCTGCCTGCT 61.795 66.667 7.50 7.50 37.84 4.24
1276 1398 3.441290 CTGCCTGCCTGCTTGCTC 61.441 66.667 5.36 0.00 0.00 4.26
1407 1586 2.577563 ACCATGTGTCTGGATGATTGGA 59.422 45.455 0.00 0.00 39.73 3.53
1408 1587 3.203710 ACCATGTGTCTGGATGATTGGAT 59.796 43.478 0.00 0.00 39.73 3.41
1409 1588 3.819337 CCATGTGTCTGGATGATTGGATC 59.181 47.826 0.00 0.00 38.69 3.36
1410 1589 3.183793 TGTGTCTGGATGATTGGATCG 57.816 47.619 0.00 0.00 0.00 3.69
1411 1590 2.158914 TGTGTCTGGATGATTGGATCGG 60.159 50.000 0.00 0.00 0.00 4.18
1485 1664 2.237143 TGACCAATCAACCTCCAGCTAG 59.763 50.000 0.00 0.00 0.00 3.42
1486 1665 1.065126 ACCAATCAACCTCCAGCTAGC 60.065 52.381 6.62 6.62 0.00 3.42
1488 1667 2.559440 CAATCAACCTCCAGCTAGCTC 58.441 52.381 16.15 0.00 0.00 4.09
1489 1668 1.127343 ATCAACCTCCAGCTAGCTCC 58.873 55.000 16.15 0.00 0.00 4.70
1490 1669 0.041833 TCAACCTCCAGCTAGCTCCT 59.958 55.000 16.15 0.00 0.00 3.69
1492 1671 1.280421 CAACCTCCAGCTAGCTCCTTT 59.720 52.381 16.15 0.92 0.00 3.11
1493 1672 1.662686 ACCTCCAGCTAGCTCCTTTT 58.337 50.000 16.15 0.00 0.00 2.27
1495 1674 1.836802 CCTCCAGCTAGCTCCTTTTCT 59.163 52.381 16.15 0.00 0.00 2.52
1496 1675 2.419851 CCTCCAGCTAGCTCCTTTTCTG 60.420 54.545 16.15 1.36 0.00 3.02
1497 1676 2.499289 CTCCAGCTAGCTCCTTTTCTGA 59.501 50.000 16.15 0.91 0.00 3.27
1498 1677 2.906389 TCCAGCTAGCTCCTTTTCTGAA 59.094 45.455 16.15 0.00 0.00 3.02
1499 1678 3.327757 TCCAGCTAGCTCCTTTTCTGAAA 59.672 43.478 16.15 0.00 0.00 2.69
1500 1679 4.074970 CCAGCTAGCTCCTTTTCTGAAAA 58.925 43.478 16.15 14.31 0.00 2.29
1501 1680 4.520492 CCAGCTAGCTCCTTTTCTGAAAAA 59.480 41.667 16.15 2.58 33.42 1.94
1543 1722 1.194781 AGTATAGCCAGCCCGGATGG 61.195 60.000 18.03 18.03 42.66 3.51
1562 1743 5.397899 GGATGGTGAGGGAATGATCAAAGTA 60.398 44.000 0.00 0.00 0.00 2.24
1566 1747 4.884164 GTGAGGGAATGATCAAAGTAAGGG 59.116 45.833 0.00 0.00 0.00 3.95
1569 1750 3.954258 GGGAATGATCAAAGTAAGGGTGG 59.046 47.826 0.00 0.00 0.00 4.61
1571 1752 3.737559 ATGATCAAAGTAAGGGTGGCA 57.262 42.857 0.00 0.00 0.00 4.92
1577 1758 6.770785 TGATCAAAGTAAGGGTGGCATATTAC 59.229 38.462 0.00 9.93 0.00 1.89
1580 1761 5.362105 AAGTAAGGGTGGCATATTACGAA 57.638 39.130 11.36 0.00 34.17 3.85
1581 1762 5.562298 AGTAAGGGTGGCATATTACGAAT 57.438 39.130 11.36 0.00 34.17 3.34
1582 1763 5.937111 AGTAAGGGTGGCATATTACGAATT 58.063 37.500 11.36 0.00 34.17 2.17
1583 1764 6.362248 AGTAAGGGTGGCATATTACGAATTT 58.638 36.000 11.36 0.00 34.17 1.82
1584 1765 7.511268 AGTAAGGGTGGCATATTACGAATTTA 58.489 34.615 11.36 0.00 34.17 1.40
1585 1766 6.628919 AAGGGTGGCATATTACGAATTTAC 57.371 37.500 0.00 0.00 0.00 2.01
1596 1777 5.540400 TTACGAATTTACGAGGGATGGAT 57.460 39.130 0.00 0.00 37.03 3.41
1620 1805 5.163478 TGGATGCATGATCGATCGATAATCT 60.163 40.000 29.45 14.52 34.60 2.40
1652 1843 0.824759 ACGAGGGATCACCAAGTAGC 59.175 55.000 0.00 0.00 43.89 3.58
1676 1867 7.038445 AGCAGTACTAGCAGATGGAATGAATAT 60.038 37.037 16.27 0.00 0.00 1.28
1681 1872 7.160049 ACTAGCAGATGGAATGAATATGAGTG 58.840 38.462 0.00 0.00 0.00 3.51
1708 1906 0.178068 AATCGGGATCGGTGGTTGAG 59.822 55.000 0.00 0.00 36.95 3.02
1716 1914 2.297698 TCGGTGGTTGAGAAGAGGTA 57.702 50.000 0.00 0.00 0.00 3.08
1736 1941 9.802039 AGAGGTATTTGTTAACACCATCTAAAA 57.198 29.630 8.07 0.00 33.27 1.52
1765 1970 2.287915 CACGCATGAGCTAACCCATAAC 59.712 50.000 0.00 0.00 39.10 1.89
1767 1972 1.264288 GCATGAGCTAACCCATAACGC 59.736 52.381 0.00 0.00 37.91 4.84
1768 1973 1.526887 CATGAGCTAACCCATAACGCG 59.473 52.381 3.53 3.53 0.00 6.01
1769 1974 0.533491 TGAGCTAACCCATAACGCGT 59.467 50.000 5.58 5.58 0.00 6.01
1876 2107 7.715265 AAGATAACATCTAACCATAGCAACG 57.285 36.000 0.00 0.00 39.08 4.10
1878 2109 7.148641 AGATAACATCTAACCATAGCAACGAG 58.851 38.462 0.00 0.00 38.00 4.18
1924 2155 8.565896 TCATGCAACAGTTCATAAACTTAGAT 57.434 30.769 0.00 0.00 43.28 1.98
1925 2156 8.668353 TCATGCAACAGTTCATAAACTTAGATC 58.332 33.333 0.00 0.00 43.28 2.75
1998 2236 4.572909 ACTGTGGTTATTTTCCTACGACC 58.427 43.478 0.00 0.00 0.00 4.79
2034 2273 5.867716 AGTATAACGTTGTGTCATGGAAGAC 59.132 40.000 11.99 0.00 38.99 3.01
2049 2288 4.127171 TGGAAGACGAAAGAGTTTGAAGG 58.873 43.478 0.00 0.00 0.00 3.46
2054 2293 4.099573 AGACGAAAGAGTTTGAAGGTCTCA 59.900 41.667 0.00 0.00 0.00 3.27
2126 2365 1.186030 CGACGGTATCAAGTGTACGC 58.814 55.000 0.00 0.00 0.00 4.42
2127 2366 1.202110 CGACGGTATCAAGTGTACGCT 60.202 52.381 2.24 2.24 0.00 5.07
2133 2372 2.579207 ATCAAGTGTACGCTACGCAT 57.421 45.000 9.84 0.00 41.48 4.73
2134 2373 1.624487 TCAAGTGTACGCTACGCATG 58.376 50.000 9.84 4.02 41.48 4.06
2239 2478 0.034337 GGTACAAGCCGGTCTCAACA 59.966 55.000 1.90 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.823281 TCTAACAACTCCACGAAACCA 57.177 42.857 0.00 0.00 0.00 3.67
1 2 4.062991 ACATCTAACAACTCCACGAAACC 58.937 43.478 0.00 0.00 0.00 3.27
10 11 4.816925 GGATAGGGCAACATCTAACAACTC 59.183 45.833 0.00 0.00 39.74 3.01
84 86 1.212751 GTGCCATTTCCGGTTGCTC 59.787 57.895 0.00 0.00 0.00 4.26
87 89 1.288752 GTGGTGCCATTTCCGGTTG 59.711 57.895 0.00 0.00 0.00 3.77
91 93 1.603455 ACCTGTGGTGCCATTTCCG 60.603 57.895 0.00 0.00 32.98 4.30
152 156 6.094603 CCACTAGAGATTCCAAAAGTCCATTG 59.905 42.308 0.00 0.00 0.00 2.82
275 281 9.185192 CAAATTCACCAGAATAGAAAAACAGAC 57.815 33.333 0.00 0.00 43.52 3.51
293 301 6.091441 ACGCTCTATCTGAACTTCAAATTCAC 59.909 38.462 0.00 0.00 32.67 3.18
421 434 6.913009 ACTGCAGGAGTATTATGGGACAGAC 61.913 48.000 19.93 0.00 35.14 3.51
424 437 3.134623 CACTGCAGGAGTATTATGGGACA 59.865 47.826 19.93 0.00 36.32 4.02
487 583 5.310720 AGAACCAAAATATCCGCAAAGAC 57.689 39.130 0.00 0.00 0.00 3.01
561 664 4.702131 AGAGCACTGAAAACAAACTGAACT 59.298 37.500 0.00 0.00 0.00 3.01
595 698 6.403866 ACAAGTGGATAAAACAGAAATGCA 57.596 33.333 0.00 0.00 0.00 3.96
603 706 9.787435 ATAACTGTCTAACAAGTGGATAAAACA 57.213 29.630 0.00 0.00 0.00 2.83
620 723 6.435292 ACAAGGGTCTGTTTATAACTGTCT 57.565 37.500 0.00 0.00 0.00 3.41
621 724 7.118825 GGTTACAAGGGTCTGTTTATAACTGTC 59.881 40.741 0.00 0.00 0.00 3.51
622 725 6.938596 GGTTACAAGGGTCTGTTTATAACTGT 59.061 38.462 0.00 0.00 0.00 3.55
623 726 7.166167 AGGTTACAAGGGTCTGTTTATAACTG 58.834 38.462 0.00 0.00 0.00 3.16
624 727 7.325725 AGGTTACAAGGGTCTGTTTATAACT 57.674 36.000 0.00 0.00 0.00 2.24
625 728 7.991084 AAGGTTACAAGGGTCTGTTTATAAC 57.009 36.000 0.00 0.00 0.00 1.89
627 730 9.675464 CAATAAGGTTACAAGGGTCTGTTTATA 57.325 33.333 0.00 0.00 0.00 0.98
628 731 7.614192 CCAATAAGGTTACAAGGGTCTGTTTAT 59.386 37.037 0.00 0.00 0.00 1.40
629 732 6.943718 CCAATAAGGTTACAAGGGTCTGTTTA 59.056 38.462 0.00 0.00 0.00 2.01
630 733 5.773176 CCAATAAGGTTACAAGGGTCTGTTT 59.227 40.000 0.00 0.00 0.00 2.83
631 734 5.073965 TCCAATAAGGTTACAAGGGTCTGTT 59.926 40.000 0.00 0.00 39.02 3.16
632 735 4.600111 TCCAATAAGGTTACAAGGGTCTGT 59.400 41.667 0.00 0.00 39.02 3.41
633 736 5.045869 TCTCCAATAAGGTTACAAGGGTCTG 60.046 44.000 0.00 0.00 39.02 3.51
634 737 5.098663 TCTCCAATAAGGTTACAAGGGTCT 58.901 41.667 0.00 0.00 39.02 3.85
635 738 5.431179 TCTCCAATAAGGTTACAAGGGTC 57.569 43.478 0.00 0.00 39.02 4.46
636 739 5.806734 GCTTCTCCAATAAGGTTACAAGGGT 60.807 44.000 0.00 0.00 39.02 4.34
637 740 4.640647 GCTTCTCCAATAAGGTTACAAGGG 59.359 45.833 0.00 0.00 39.02 3.95
638 741 5.253330 TGCTTCTCCAATAAGGTTACAAGG 58.747 41.667 0.00 0.00 39.02 3.61
639 742 6.817765 TTGCTTCTCCAATAAGGTTACAAG 57.182 37.500 0.00 0.00 39.02 3.16
640 743 7.001674 TCTTTGCTTCTCCAATAAGGTTACAA 58.998 34.615 0.00 0.00 39.02 2.41
641 744 6.539173 TCTTTGCTTCTCCAATAAGGTTACA 58.461 36.000 0.00 0.00 39.02 2.41
642 745 7.448748 TTCTTTGCTTCTCCAATAAGGTTAC 57.551 36.000 0.00 0.00 39.02 2.50
643 746 8.472007 TTTTCTTTGCTTCTCCAATAAGGTTA 57.528 30.769 0.00 0.00 39.02 2.85
644 747 6.976934 TTTCTTTGCTTCTCCAATAAGGTT 57.023 33.333 0.00 0.00 39.02 3.50
645 748 6.976934 TTTTCTTTGCTTCTCCAATAAGGT 57.023 33.333 0.00 0.00 39.02 3.50
646 749 7.209475 TGTTTTTCTTTGCTTCTCCAATAAGG 58.791 34.615 0.00 0.00 39.47 2.69
647 750 7.095899 GCTGTTTTTCTTTGCTTCTCCAATAAG 60.096 37.037 0.00 0.00 0.00 1.73
648 751 6.701400 GCTGTTTTTCTTTGCTTCTCCAATAA 59.299 34.615 0.00 0.00 0.00 1.40
649 752 6.183360 TGCTGTTTTTCTTTGCTTCTCCAATA 60.183 34.615 0.00 0.00 0.00 1.90
650 753 5.052481 GCTGTTTTTCTTTGCTTCTCCAAT 58.948 37.500 0.00 0.00 0.00 3.16
651 754 4.081752 TGCTGTTTTTCTTTGCTTCTCCAA 60.082 37.500 0.00 0.00 0.00 3.53
685 788 5.383130 GCTCGACTTTGGTTCAAATACTTC 58.617 41.667 0.00 0.00 32.70 3.01
776 879 3.412408 GGTGGAAGAGCCCTCCCC 61.412 72.222 0.00 0.00 34.58 4.81
778 881 2.610859 TGGGTGGAAGAGCCCTCC 60.611 66.667 0.00 0.00 45.06 4.30
779 882 2.190488 CTGTGGGTGGAAGAGCCCTC 62.190 65.000 0.00 0.00 45.06 4.30
780 883 2.121963 TGTGGGTGGAAGAGCCCT 60.122 61.111 0.00 0.00 45.06 5.19
799 902 2.263741 GCTTCTGTGTGCCCTGTGG 61.264 63.158 0.00 0.00 0.00 4.17
801 904 1.526917 GTGCTTCTGTGTGCCCTGT 60.527 57.895 0.00 0.00 0.00 4.00
803 906 1.072159 GAGTGCTTCTGTGTGCCCT 59.928 57.895 0.00 0.00 0.00 5.19
804 907 1.227943 TGAGTGCTTCTGTGTGCCC 60.228 57.895 0.00 0.00 0.00 5.36
806 909 2.154854 TAGTGAGTGCTTCTGTGTGC 57.845 50.000 0.00 0.00 0.00 4.57
807 910 8.352942 TGTATATATAGTGAGTGCTTCTGTGTG 58.647 37.037 0.00 0.00 0.00 3.82
808 911 8.465273 TGTATATATAGTGAGTGCTTCTGTGT 57.535 34.615 0.00 0.00 0.00 3.72
809 912 7.540400 GCTGTATATATAGTGAGTGCTTCTGTG 59.460 40.741 8.15 0.00 0.00 3.66
821 924 6.712241 GTGCAACCTGCTGTATATATAGTG 57.288 41.667 8.15 0.29 45.31 2.74
839 946 1.462616 CGGAGGAATGAATGGTGCAA 58.537 50.000 0.00 0.00 0.00 4.08
842 949 1.019673 CTGCGGAGGAATGAATGGTG 58.980 55.000 0.00 0.00 0.00 4.17
843 950 0.749454 GCTGCGGAGGAATGAATGGT 60.749 55.000 5.93 0.00 0.00 3.55
844 951 0.749091 TGCTGCGGAGGAATGAATGG 60.749 55.000 5.93 0.00 0.00 3.16
847 954 0.674581 CTGTGCTGCGGAGGAATGAA 60.675 55.000 5.93 0.00 0.00 2.57
848 955 1.078918 CTGTGCTGCGGAGGAATGA 60.079 57.895 5.93 0.00 0.00 2.57
854 961 2.814341 CTGAGCTGTGCTGCGGAG 60.814 66.667 0.00 0.00 39.88 4.63
866 973 2.433318 GAGACGGTGTGCCTGAGC 60.433 66.667 0.00 0.00 40.48 4.26
867 974 0.389166 GAAGAGACGGTGTGCCTGAG 60.389 60.000 0.00 0.00 0.00 3.35
868 975 1.666011 GAAGAGACGGTGTGCCTGA 59.334 57.895 0.00 0.00 0.00 3.86
869 976 1.374758 GGAAGAGACGGTGTGCCTG 60.375 63.158 0.00 0.00 0.00 4.85
870 977 1.534235 AGGAAGAGACGGTGTGCCT 60.534 57.895 0.00 0.00 0.00 4.75
873 980 0.900647 AGGGAGGAAGAGACGGTGTG 60.901 60.000 0.00 0.00 0.00 3.82
874 981 0.612453 GAGGGAGGAAGAGACGGTGT 60.612 60.000 0.00 0.00 0.00 4.16
875 982 1.324005 GGAGGGAGGAAGAGACGGTG 61.324 65.000 0.00 0.00 0.00 4.94
876 983 1.000612 GGAGGGAGGAAGAGACGGT 59.999 63.158 0.00 0.00 0.00 4.83
884 991 2.913617 GAGAAAGAAAGGGAGGGAGGAA 59.086 50.000 0.00 0.00 0.00 3.36
887 994 1.562008 GGGAGAAAGAAAGGGAGGGAG 59.438 57.143 0.00 0.00 0.00 4.30
894 1001 4.202472 ACCACTAACAGGGAGAAAGAAAGG 60.202 45.833 0.00 0.00 0.00 3.11
895 1002 4.974399 ACCACTAACAGGGAGAAAGAAAG 58.026 43.478 0.00 0.00 0.00 2.62
896 1003 4.502604 CGACCACTAACAGGGAGAAAGAAA 60.503 45.833 0.00 0.00 0.00 2.52
897 1004 3.006537 CGACCACTAACAGGGAGAAAGAA 59.993 47.826 0.00 0.00 0.00 2.52
898 1005 2.561419 CGACCACTAACAGGGAGAAAGA 59.439 50.000 0.00 0.00 0.00 2.52
922 1029 0.036671 GTAGGTGGGTGCTGTGTACC 60.037 60.000 0.00 0.00 37.58 3.34
959 1066 3.678289 TCAACCTAGTGCTCGTGTACTA 58.322 45.455 13.55 13.55 39.73 1.82
960 1067 2.511659 TCAACCTAGTGCTCGTGTACT 58.488 47.619 12.72 12.72 41.81 2.73
961 1068 3.505464 ATCAACCTAGTGCTCGTGTAC 57.495 47.619 0.00 0.00 0.00 2.90
962 1069 3.630769 CCTATCAACCTAGTGCTCGTGTA 59.369 47.826 0.00 0.00 0.00 2.90
963 1070 2.427453 CCTATCAACCTAGTGCTCGTGT 59.573 50.000 0.00 0.00 0.00 4.49
964 1071 2.799917 GCCTATCAACCTAGTGCTCGTG 60.800 54.545 0.00 0.00 0.00 4.35
965 1072 1.409427 GCCTATCAACCTAGTGCTCGT 59.591 52.381 0.00 0.00 0.00 4.18
966 1073 1.409064 TGCCTATCAACCTAGTGCTCG 59.591 52.381 0.00 0.00 0.00 5.03
967 1074 2.224161 CCTGCCTATCAACCTAGTGCTC 60.224 54.545 0.00 0.00 0.00 4.26
968 1075 1.765314 CCTGCCTATCAACCTAGTGCT 59.235 52.381 0.00 0.00 0.00 4.40
969 1076 1.762957 TCCTGCCTATCAACCTAGTGC 59.237 52.381 0.00 0.00 0.00 4.40
970 1077 2.224161 GCTCCTGCCTATCAACCTAGTG 60.224 54.545 0.00 0.00 0.00 2.74
971 1078 2.043227 GCTCCTGCCTATCAACCTAGT 58.957 52.381 0.00 0.00 0.00 2.57
972 1079 2.036992 CAGCTCCTGCCTATCAACCTAG 59.963 54.545 0.00 0.00 40.80 3.02
973 1080 2.042464 CAGCTCCTGCCTATCAACCTA 58.958 52.381 0.00 0.00 40.80 3.08
974 1081 0.835941 CAGCTCCTGCCTATCAACCT 59.164 55.000 0.00 0.00 40.80 3.50
975 1082 0.833287 TCAGCTCCTGCCTATCAACC 59.167 55.000 0.00 0.00 40.80 3.77
976 1083 2.926778 ATCAGCTCCTGCCTATCAAC 57.073 50.000 0.00 0.00 40.80 3.18
977 1084 3.517100 GGATATCAGCTCCTGCCTATCAA 59.483 47.826 4.83 0.00 40.80 2.57
978 1085 3.102972 GGATATCAGCTCCTGCCTATCA 58.897 50.000 4.83 0.00 40.80 2.15
1065 1181 4.740822 ACCACCATCGGCTTGGCC 62.741 66.667 0.00 0.00 46.75 5.36
1095 1211 1.809619 CACGTACATGAGGCACCGG 60.810 63.158 0.00 0.00 0.00 5.28
1225 1347 1.455587 CCTGCCTGTTGGTGTTGGT 60.456 57.895 0.00 0.00 35.27 3.67
1271 1393 3.368116 GGTAAGAAAGGAGTAGCGAGCAA 60.368 47.826 0.00 0.00 0.00 3.91
1276 1398 1.138464 GGGGGTAAGAAAGGAGTAGCG 59.862 57.143 0.00 0.00 0.00 4.26
1407 1586 3.804325 CAGAAATAGTCGTGCAATCCGAT 59.196 43.478 0.98 0.00 36.62 4.18
1408 1587 3.186909 CAGAAATAGTCGTGCAATCCGA 58.813 45.455 0.00 0.00 0.00 4.55
1409 1588 2.285834 GCAGAAATAGTCGTGCAATCCG 60.286 50.000 0.00 0.00 35.91 4.18
1410 1589 2.939103 AGCAGAAATAGTCGTGCAATCC 59.061 45.455 0.00 0.00 38.44 3.01
1411 1590 3.868077 AGAGCAGAAATAGTCGTGCAATC 59.132 43.478 0.00 0.00 38.44 2.67
1463 1642 1.637553 AGCTGGAGGTTGATTGGTCAT 59.362 47.619 0.00 0.00 33.56 3.06
1469 1648 1.488393 GGAGCTAGCTGGAGGTTGATT 59.512 52.381 24.99 0.00 0.00 2.57
1501 1680 4.709250 GCTATAGCTAGCTGGAGGTTTTT 58.291 43.478 27.68 0.00 45.78 1.94
1502 1681 4.344359 GCTATAGCTAGCTGGAGGTTTT 57.656 45.455 27.68 0.00 45.78 2.43
1517 1696 2.099921 CGGGCTGGCTATACTGCTATAG 59.900 54.545 0.00 0.00 36.39 1.31
1518 1697 2.100197 CGGGCTGGCTATACTGCTATA 58.900 52.381 0.00 0.00 35.86 1.31
1519 1698 0.898320 CGGGCTGGCTATACTGCTAT 59.102 55.000 0.00 0.00 35.86 2.97
1520 1699 1.185618 CCGGGCTGGCTATACTGCTA 61.186 60.000 0.00 0.00 35.86 3.49
1543 1722 4.884164 CCCTTACTTTGATCATTCCCTCAC 59.116 45.833 0.00 0.00 0.00 3.51
1550 1731 4.046286 TGCCACCCTTACTTTGATCATT 57.954 40.909 0.00 0.00 0.00 2.57
1562 1743 5.237779 CGTAAATTCGTAATATGCCACCCTT 59.762 40.000 0.00 0.00 0.00 3.95
1566 1747 5.107220 CCCTCGTAAATTCGTAATATGCCAC 60.107 44.000 0.00 0.00 0.00 5.01
1569 1750 6.183360 CCATCCCTCGTAAATTCGTAATATGC 60.183 42.308 0.00 0.00 0.00 3.14
1571 1752 7.235935 TCCATCCCTCGTAAATTCGTAATAT 57.764 36.000 0.00 0.00 0.00 1.28
1577 1758 3.067106 CCATCCATCCCTCGTAAATTCG 58.933 50.000 0.00 0.00 0.00 3.34
1580 1761 3.560025 GCATCCATCCATCCCTCGTAAAT 60.560 47.826 0.00 0.00 0.00 1.40
1581 1762 2.224523 GCATCCATCCATCCCTCGTAAA 60.225 50.000 0.00 0.00 0.00 2.01
1582 1763 1.347707 GCATCCATCCATCCCTCGTAA 59.652 52.381 0.00 0.00 0.00 3.18
1583 1764 0.976641 GCATCCATCCATCCCTCGTA 59.023 55.000 0.00 0.00 0.00 3.43
1584 1765 1.056125 TGCATCCATCCATCCCTCGT 61.056 55.000 0.00 0.00 0.00 4.18
1585 1766 0.327259 ATGCATCCATCCATCCCTCG 59.673 55.000 0.00 0.00 0.00 4.63
1596 1777 4.454728 TTATCGATCGATCATGCATCCA 57.545 40.909 32.50 10.48 36.17 3.41
1620 1805 1.411977 TCCCTCGTTAAAACCGTCACA 59.588 47.619 0.00 0.00 0.00 3.58
1652 1843 8.309656 TCATATTCATTCCATCTGCTAGTACTG 58.690 37.037 5.39 0.00 0.00 2.74
1676 1867 3.694043 TCCCGATTCAATTGTCACTCA 57.306 42.857 5.13 0.00 0.00 3.41
1681 1872 2.287915 CACCGATCCCGATTCAATTGTC 59.712 50.000 5.13 0.00 38.22 3.18
1708 1906 7.923414 AGATGGTGTTAACAAATACCTCTTC 57.077 36.000 10.51 6.48 34.32 2.87
1736 1941 4.142600 GGTTAGCTCATGCGTGATTCTTTT 60.143 41.667 9.53 0.00 45.42 2.27
1875 2106 3.427773 GGGTGTTGTAACTCTAGAGCTCG 60.428 52.174 19.97 0.00 0.00 5.03
1876 2107 3.119065 GGGGTGTTGTAACTCTAGAGCTC 60.119 52.174 19.97 5.27 0.00 4.09
1878 2109 2.832733 AGGGGTGTTGTAACTCTAGAGC 59.167 50.000 19.97 4.30 0.00 4.09
1889 2120 0.106268 TGTTGCATGAGGGGTGTTGT 60.106 50.000 0.00 0.00 0.00 3.32
1924 2155 1.278985 TCCTACGGTTCTCCTGTACGA 59.721 52.381 0.00 0.00 0.00 3.43
1925 2156 1.669779 CTCCTACGGTTCTCCTGTACG 59.330 57.143 0.00 0.00 0.00 3.67
2017 2256 1.778334 TCGTCTTCCATGACACAACG 58.222 50.000 0.00 0.00 36.82 4.10
2049 2288 5.349824 AGAAACGAGCAAATCTTTGAGAC 57.650 39.130 6.84 0.00 40.55 3.36
2054 2293 7.931275 AGTCTAAAAGAAACGAGCAAATCTTT 58.069 30.769 0.00 0.00 42.30 2.52
2101 2340 5.276820 CGTACACTTGATACCGTCGTATACA 60.277 44.000 3.32 0.00 35.23 2.29
2103 2342 4.318760 GCGTACACTTGATACCGTCGTATA 60.319 45.833 0.00 0.00 35.23 1.47
2126 2365 6.603237 TGACTCATTTAAATCCATGCGTAG 57.397 37.500 0.00 0.00 0.00 3.51
2127 2366 7.095816 CGTATGACTCATTTAAATCCATGCGTA 60.096 37.037 19.47 6.88 35.22 4.42
2133 2372 5.996644 ACCCGTATGACTCATTTAAATCCA 58.003 37.500 0.00 0.00 0.00 3.41
2134 2373 6.937436 AACCCGTATGACTCATTTAAATCC 57.063 37.500 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.