Multiple sequence alignment - TraesCS5B01G073400

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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 TraesCS5B01G073400 chr5B 100.000 3917 0 0 1 3917 87238247 87242163 0.000000e+00 7234.0
1 TraesCS5B01G073400 chr5B 88.875 782 35 11 1 770 493925649 493926390 0.000000e+00 915.0
2 TraesCS5B01G073400 chr5B 83.444 151 16 4 1121 1262 83617101 83616951 8.830000e-27 132.0
3 TraesCS5B01G073400 chr5B 83.673 147 15 7 1124 1261 83620971 83620825 3.180000e-26 130.0
4 TraesCS5B01G073400 chr5D 88.724 2625 202 56 769 3318 77586096 77588701 0.000000e+00 3121.0
5 TraesCS5B01G073400 chr5D 92.269 802 34 9 1 777 410393239 410392441 0.000000e+00 1112.0
6 TraesCS5B01G073400 chr5D 94.830 619 19 9 3302 3917 77590378 77590986 0.000000e+00 953.0
7 TraesCS5B01G073400 chr5D 82.022 356 51 8 1579 1925 76204420 76204069 1.380000e-74 291.0
8 TraesCS5B01G073400 chr5D 88.000 100 9 1 1166 1262 75277381 75277282 8.890000e-22 115.0
9 TraesCS5B01G073400 chr5D 86.667 75 10 0 2753 2827 78013017 78013091 2.510000e-12 84.2
10 TraesCS5B01G073400 chr5A 88.714 2419 134 49 767 3144 74486178 74488498 0.000000e+00 2826.0
11 TraesCS5B01G073400 chr5A 92.339 744 44 1 1 731 557070584 557071327 0.000000e+00 1046.0
12 TraesCS5B01G073400 chr5A 86.219 283 20 7 3269 3538 74488791 74489067 4.950000e-74 289.0
13 TraesCS5B01G073400 chr5A 90.476 105 10 0 3747 3851 74489613 74489717 5.280000e-29 139.0
14 TraesCS5B01G073400 chr5A 83.221 149 16 4 1123 1262 70463233 70463085 1.140000e-25 128.0
15 TraesCS5B01G073400 chr5A 84.746 118 15 1 1148 1262 70459352 70459235 8.890000e-22 115.0
16 TraesCS5B01G073400 chr3B 94.665 731 36 1 1 731 104968628 104967901 0.000000e+00 1131.0
17 TraesCS5B01G073400 chr3D 92.453 795 30 10 7 774 352946246 352945455 0.000000e+00 1109.0
18 TraesCS5B01G073400 chr3D 91.519 790 41 5 3 768 83700486 83699699 0.000000e+00 1064.0
19 TraesCS5B01G073400 chr1A 92.191 794 38 4 1 770 432517016 432517809 0.000000e+00 1101.0
20 TraesCS5B01G073400 chr1A 88.564 787 49 17 1 767 544379885 544379120 0.000000e+00 917.0
21 TraesCS5B01G073400 chr7D 91.803 793 39 4 1 768 414431539 414432330 0.000000e+00 1081.0
22 TraesCS5B01G073400 chr7D 91.288 792 33 12 1 771 159701662 159702438 0.000000e+00 1048.0
23 TraesCS5B01G073400 chr2D 91.646 790 30 11 1 770 201455842 201456615 0.000000e+00 1061.0
24 TraesCS5B01G073400 chr4D 91.001 789 35 13 1 768 85888121 85888894 0.000000e+00 1031.0
25 TraesCS5B01G073400 chr7A 91.812 745 48 3 1 732 711959839 711960583 0.000000e+00 1026.0
26 TraesCS5B01G073400 chr2B 90.064 785 46 14 1 770 712759506 712760273 0.000000e+00 989.0
27 TraesCS5B01G073400 chr2B 89.381 791 58 11 1 769 549297037 549297823 0.000000e+00 972.0
28 TraesCS5B01G073400 chr1D 89.747 790 43 14 1 768 471206336 471207109 0.000000e+00 976.0
29 TraesCS5B01G073400 chr4A 92.869 589 40 2 1981 2568 665446453 665445866 0.000000e+00 854.0
30 TraesCS5B01G073400 chr4A 91.750 400 27 3 2589 2985 665445710 665445314 5.720000e-153 551.0
31 TraesCS5B01G073400 chr4A 95.349 215 8 2 1573 1786 665446853 665446640 1.350000e-89 340.0
32 TraesCS5B01G073400 chr4A 93.923 181 11 0 1742 1922 665446641 665446461 1.390000e-69 274.0
33 TraesCS5B01G073400 chr6B 91.759 449 35 2 2121 2568 181104532 181104085 1.200000e-174 623.0
34 TraesCS5B01G073400 chr6B 94.872 351 16 2 1573 1922 181105095 181104746 7.400000e-152 547.0
35 TraesCS5B01G073400 chr6B 91.500 400 28 3 2589 2985 181103929 181103533 2.660000e-151 545.0
36 TraesCS5B01G073400 chr6B 95.588 204 9 0 1981 2184 181104738 181104535 1.050000e-85 327.0
37 TraesCS5B01G073400 chr4B 98.361 61 1 0 711 771 481524887 481524827 1.490000e-19 108.0


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 TraesCS5B01G073400 chr5B 87238247 87242163 3916 False 7234.000000 7234 100.000000 1 3917 1 chr5B.!!$F1 3916
1 TraesCS5B01G073400 chr5B 493925649 493926390 741 False 915.000000 915 88.875000 1 770 1 chr5B.!!$F2 769
2 TraesCS5B01G073400 chr5D 77586096 77590986 4890 False 2037.000000 3121 91.777000 769 3917 2 chr5D.!!$F2 3148
3 TraesCS5B01G073400 chr5D 410392441 410393239 798 True 1112.000000 1112 92.269000 1 777 1 chr5D.!!$R3 776
4 TraesCS5B01G073400 chr5A 74486178 74489717 3539 False 1084.666667 2826 88.469667 767 3851 3 chr5A.!!$F2 3084
5 TraesCS5B01G073400 chr5A 557070584 557071327 743 False 1046.000000 1046 92.339000 1 731 1 chr5A.!!$F1 730
6 TraesCS5B01G073400 chr3B 104967901 104968628 727 True 1131.000000 1131 94.665000 1 731 1 chr3B.!!$R1 730
7 TraesCS5B01G073400 chr3D 352945455 352946246 791 True 1109.000000 1109 92.453000 7 774 1 chr3D.!!$R2 767
8 TraesCS5B01G073400 chr3D 83699699 83700486 787 True 1064.000000 1064 91.519000 3 768 1 chr3D.!!$R1 765
9 TraesCS5B01G073400 chr1A 432517016 432517809 793 False 1101.000000 1101 92.191000 1 770 1 chr1A.!!$F1 769
10 TraesCS5B01G073400 chr1A 544379120 544379885 765 True 917.000000 917 88.564000 1 767 1 chr1A.!!$R1 766
11 TraesCS5B01G073400 chr7D 414431539 414432330 791 False 1081.000000 1081 91.803000 1 768 1 chr7D.!!$F2 767
12 TraesCS5B01G073400 chr7D 159701662 159702438 776 False 1048.000000 1048 91.288000 1 771 1 chr7D.!!$F1 770
13 TraesCS5B01G073400 chr2D 201455842 201456615 773 False 1061.000000 1061 91.646000 1 770 1 chr2D.!!$F1 769
14 TraesCS5B01G073400 chr4D 85888121 85888894 773 False 1031.000000 1031 91.001000 1 768 1 chr4D.!!$F1 767
15 TraesCS5B01G073400 chr7A 711959839 711960583 744 False 1026.000000 1026 91.812000 1 732 1 chr7A.!!$F1 731
16 TraesCS5B01G073400 chr2B 712759506 712760273 767 False 989.000000 989 90.064000 1 770 1 chr2B.!!$F2 769
17 TraesCS5B01G073400 chr2B 549297037 549297823 786 False 972.000000 972 89.381000 1 769 1 chr2B.!!$F1 768
18 TraesCS5B01G073400 chr1D 471206336 471207109 773 False 976.000000 976 89.747000 1 768 1 chr1D.!!$F1 767
19 TraesCS5B01G073400 chr4A 665445314 665446853 1539 True 504.750000 854 93.472750 1573 2985 4 chr4A.!!$R1 1412
20 TraesCS5B01G073400 chr6B 181103533 181105095 1562 True 510.500000 623 93.429750 1573 2985 4 chr6B.!!$R1 1412

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
966 1055 0.390998 GCCAGCACAACTCCTCTCTC 60.391 60.0 0.00 0.00 0.00 3.20 F
1201 1309 0.181114 TACTGGGAGCACATGGATGC 59.819 55.0 0.00 0.00 46.50 3.91 F
1967 2165 0.525455 TTCTGATGATGACGACGGCG 60.525 55.0 10.39 10.39 44.79 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1849 2032 0.102120 CGCCAGCGAAGAGAGAAGAT 59.898 55.000 6.06 0.0 42.83 2.40 R
2548 2829 0.239347 GTGCATGCCAGAGTTGACAC 59.761 55.000 16.68 0.0 0.00 3.67 R
2934 3358 1.135141 TGCCAAAATATTCAGCGCACC 60.135 47.619 11.47 0.0 0.00 5.01 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
77 78 3.075005 AGGCGGCTTTCGAGGCTA 61.075 61.111 5.25 0.00 42.43 3.93
814 874 6.408858 AAGATGAAGTAAACATAGCACACG 57.591 37.500 0.00 0.00 0.00 4.49
878 938 2.158295 ACACCCAGAGTCCACTAGTCTT 60.158 50.000 0.00 0.00 35.57 3.01
947 1036 1.063327 CTAGTCTCGTCAGCCAGCG 59.937 63.158 0.00 0.00 0.00 5.18
962 1051 3.426568 GCGCCAGCACAACTCCTC 61.427 66.667 0.00 0.00 44.35 3.71
964 1053 1.739562 CGCCAGCACAACTCCTCTC 60.740 63.158 0.00 0.00 0.00 3.20
965 1054 1.676384 GCCAGCACAACTCCTCTCT 59.324 57.895 0.00 0.00 0.00 3.10
966 1055 0.390998 GCCAGCACAACTCCTCTCTC 60.391 60.000 0.00 0.00 0.00 3.20
967 1056 1.265236 CCAGCACAACTCCTCTCTCT 58.735 55.000 0.00 0.00 0.00 3.10
968 1057 1.204467 CCAGCACAACTCCTCTCTCTC 59.796 57.143 0.00 0.00 0.00 3.20
969 1058 1.204467 CAGCACAACTCCTCTCTCTCC 59.796 57.143 0.00 0.00 0.00 3.71
1026 1116 1.803366 AAGAGCAAGGCAAGCACAGC 61.803 55.000 4.05 0.00 0.00 4.40
1027 1117 2.203451 AGCAAGGCAAGCACAGCT 60.203 55.556 4.05 0.00 42.56 4.24
1028 1118 2.197643 GAGCAAGGCAAGCACAGCTC 62.198 60.000 13.29 13.29 38.25 4.09
1029 1119 2.266627 GCAAGGCAAGCACAGCTCT 61.267 57.895 0.00 0.00 38.25 4.09
1030 1120 1.874562 CAAGGCAAGCACAGCTCTC 59.125 57.895 0.00 0.00 38.25 3.20
1031 1121 0.605860 CAAGGCAAGCACAGCTCTCT 60.606 55.000 0.00 0.00 38.25 3.10
1032 1122 0.321475 AAGGCAAGCACAGCTCTCTC 60.321 55.000 0.00 0.00 38.25 3.20
1033 1123 1.193462 AGGCAAGCACAGCTCTCTCT 61.193 55.000 0.00 0.00 38.25 3.10
1071 1161 0.454285 GTGTGTGTGTGTGTGTGTGC 60.454 55.000 0.00 0.00 0.00 4.57
1073 1163 2.277247 GTGTGTGTGTGTGTGCGC 60.277 61.111 0.00 0.00 0.00 6.09
1106 1214 0.807496 GTGGCTGAGGATGTTGCTTC 59.193 55.000 0.00 0.00 0.00 3.86
1201 1309 0.181114 TACTGGGAGCACATGGATGC 59.819 55.000 0.00 0.00 46.50 3.91
1337 1445 8.860088 ACTAGCTAGTTCCAAATTGTTGATTTT 58.140 29.630 20.95 0.00 32.33 1.82
1344 1452 5.619220 TCCAAATTGTTGATTTTCCCCTTG 58.381 37.500 0.00 0.00 35.79 3.61
1345 1453 4.216042 CCAAATTGTTGATTTTCCCCTTGC 59.784 41.667 0.00 0.00 35.79 4.01
1363 1471 5.589855 CCCTTGCAAAAAGAAAAGGATGTTT 59.410 36.000 0.00 0.00 41.49 2.83
1364 1472 6.458615 CCCTTGCAAAAAGAAAAGGATGTTTG 60.459 38.462 0.00 0.00 41.49 2.93
1374 1482 7.289587 AGAAAAGGATGTTTGAAAAACAACG 57.710 32.000 9.41 0.00 38.29 4.10
1375 1483 6.312672 AGAAAAGGATGTTTGAAAAACAACGG 59.687 34.615 9.41 0.00 38.29 4.44
1419 1528 9.695884 GATTTTCTAGAAAGCATAAAGAAGTCG 57.304 33.333 17.05 0.00 0.00 4.18
1433 1542 2.826128 AGAAGTCGTACAAGGCTCATCA 59.174 45.455 0.00 0.00 0.00 3.07
1444 1553 4.080695 ACAAGGCTCATCAGTCATGTATGT 60.081 41.667 0.00 0.00 33.66 2.29
1448 1560 5.306419 AGGCTCATCAGTCATGTATGTATGT 59.694 40.000 0.00 0.00 33.66 2.29
1467 1579 6.869388 TGTATGTATCAGAAACGCAACACTTA 59.131 34.615 0.00 0.00 0.00 2.24
1486 1598 7.463469 CACTTATGGTGTTTTCTCCAAAAAC 57.537 36.000 6.47 6.47 44.93 2.43
1553 1666 7.175990 TGGACTGTACAAACTTAAAATGGATCC 59.824 37.037 4.20 4.20 0.00 3.36
1556 1669 8.164070 ACTGTACAAACTTAAAATGGATCCTCT 58.836 33.333 14.23 0.00 0.00 3.69
1557 1670 8.335532 TGTACAAACTTAAAATGGATCCTCTG 57.664 34.615 14.23 0.00 0.00 3.35
1558 1671 7.942341 TGTACAAACTTAAAATGGATCCTCTGT 59.058 33.333 14.23 0.00 0.00 3.41
1609 1749 1.205179 TCTTAGCGCATACCGGACAAA 59.795 47.619 9.46 0.00 37.44 2.83
1667 1807 3.243359 AGGGATTTGACCTGAAAGCAA 57.757 42.857 0.00 0.00 36.85 3.91
1713 1853 1.967066 TGTTACCAAGGTTGCCAATGG 59.033 47.619 0.00 0.00 38.29 3.16
1849 2032 1.214589 GACCGGCTGCGAGAAACTA 59.785 57.895 0.00 0.00 0.00 2.24
1889 2072 1.127213 CTGGCATGCGCAAACATTTTC 59.873 47.619 17.11 0.00 41.24 2.29
1927 2110 5.480422 TCAACAGGTTGAGCAATACTCTCTA 59.520 40.000 10.63 0.00 46.41 2.43
1949 2144 9.767228 CTCTAAGTGATGATTCTGATTCTGATT 57.233 33.333 1.76 0.00 0.00 2.57
1950 2145 9.761504 TCTAAGTGATGATTCTGATTCTGATTC 57.238 33.333 7.93 7.93 0.00 2.52
1965 2163 3.048501 CTGATTCTGATGATGACGACGG 58.951 50.000 0.00 0.00 0.00 4.79
1967 2165 0.525455 TTCTGATGATGACGACGGCG 60.525 55.000 10.39 10.39 44.79 6.46
1968 2166 1.064134 CTGATGATGACGACGGCGA 59.936 57.895 22.49 0.00 41.64 5.54
1969 2167 0.932123 CTGATGATGACGACGGCGAG 60.932 60.000 22.49 10.00 41.64 5.03
1970 2168 1.658717 GATGATGACGACGGCGAGG 60.659 63.158 22.49 7.21 41.64 4.63
1971 2169 2.060004 GATGATGACGACGGCGAGGA 62.060 60.000 22.49 0.00 41.64 3.71
1972 2170 2.024871 GATGACGACGGCGAGGAG 59.975 66.667 22.49 3.86 41.64 3.69
1973 2171 3.471244 GATGACGACGGCGAGGAGG 62.471 68.421 22.49 0.00 41.64 4.30
1974 2172 3.989838 ATGACGACGGCGAGGAGGA 62.990 63.158 22.49 0.00 41.64 3.71
1975 2173 3.210528 GACGACGGCGAGGAGGAT 61.211 66.667 22.49 0.00 41.64 3.24
1976 2174 3.471244 GACGACGGCGAGGAGGATG 62.471 68.421 22.49 0.00 41.64 3.51
1977 2175 3.209812 CGACGGCGAGGAGGATGA 61.210 66.667 16.62 0.00 40.82 2.92
1978 2176 2.413765 GACGGCGAGGAGGATGAC 59.586 66.667 16.62 0.00 0.00 3.06
1979 2177 3.471244 GACGGCGAGGAGGATGACG 62.471 68.421 16.62 0.00 0.00 4.35
2001 2199 2.345876 TGATGATACAAGTGTGCCGTG 58.654 47.619 0.00 0.00 0.00 4.94
2006 2204 0.878523 TACAAGTGTGCCGTGTCAGC 60.879 55.000 0.00 0.00 37.04 4.26
2056 2254 6.655003 CCACTTTAAGGAAATTCAGTAGCAGA 59.345 38.462 0.00 0.00 0.00 4.26
2076 2281 3.826729 AGAACCAAACCAAGTAAGGCATC 59.173 43.478 0.00 0.00 0.00 3.91
2310 2591 6.094603 GTGATGTTAAGCATGAGGAAACTGAT 59.905 38.462 0.00 0.00 38.45 2.90
2328 2609 4.402155 ACTGATGAAGAGGAGAGTGATGAC 59.598 45.833 0.00 0.00 0.00 3.06
2370 2651 2.679996 TGCTACTCGAGGGCTGCA 60.680 61.111 25.19 20.72 0.00 4.41
2548 2829 6.697019 ACTTACAGCAAGCTTGTGTAATTTTG 59.303 34.615 31.70 26.18 37.83 2.44
2629 3045 0.546507 TGTGCAGGTCATCCCCAGTA 60.547 55.000 0.00 0.00 0.00 2.74
2825 3244 0.037326 TTCGAGCTGATCAAAGGCGT 60.037 50.000 0.00 0.00 0.00 5.68
2842 3264 2.275318 GCGTGAGGAATGAGAAGAAGG 58.725 52.381 0.00 0.00 0.00 3.46
2843 3265 2.275318 CGTGAGGAATGAGAAGAAGGC 58.725 52.381 0.00 0.00 0.00 4.35
2885 3307 1.209019 CCATGTTGTCAGGAGGAGGAG 59.791 57.143 0.00 0.00 0.00 3.69
2934 3358 0.109342 AAGTTCCTGCAGTGTGGGAG 59.891 55.000 13.81 0.00 0.00 4.30
3022 3450 4.669700 TGAACTGGAGTACTTAGCTGGTA 58.330 43.478 0.00 0.00 0.00 3.25
3051 3479 3.066621 GTGTGCTGAATGTTTCTGAACCA 59.933 43.478 0.00 0.00 36.59 3.67
3081 3512 5.633830 AATCACCACTGATCATCAACAAC 57.366 39.130 0.00 0.00 35.96 3.32
3095 3526 1.092921 AACAACGTCTTTCCGCTGCA 61.093 50.000 0.00 0.00 0.00 4.41
3112 3543 0.749454 GCACCCCCATGAGATGTGAC 60.749 60.000 0.00 0.00 0.00 3.67
3151 3582 9.449719 AAGACTAAGGGTTCATAGTTTTATGTG 57.550 33.333 0.00 0.00 38.25 3.21
3270 3707 7.495934 ACAGTGGTTATGTCTTCAACTATATGC 59.504 37.037 0.00 0.00 0.00 3.14
3378 5541 5.342525 GCGTGTGTCGATATAGTGGATTTAG 59.657 44.000 0.00 0.00 42.86 1.85
3455 5619 3.921119 TGGTTGATCAAACTCACATGC 57.079 42.857 23.46 1.93 38.92 4.06
3496 5664 0.464036 TGTCTGCACGAGAACCAACT 59.536 50.000 0.00 0.00 30.26 3.16
3497 5665 1.134521 TGTCTGCACGAGAACCAACTT 60.135 47.619 0.00 0.00 30.26 2.66
3537 5707 2.644299 AGTTTCAGGGTCATCCATGTGA 59.356 45.455 0.00 0.00 44.71 3.58
3538 5708 2.749621 GTTTCAGGGTCATCCATGTGAC 59.250 50.000 7.72 7.72 44.71 3.67
3545 5715 2.715046 GTCATCCATGTGACCATGTGT 58.285 47.619 5.37 0.00 45.83 3.72
3546 5716 2.421073 GTCATCCATGTGACCATGTGTG 59.579 50.000 5.37 1.44 45.83 3.82
3547 5717 2.040145 TCATCCATGTGACCATGTGTGT 59.960 45.455 2.38 0.00 45.83 3.72
3548 5718 1.894881 TCCATGTGACCATGTGTGTG 58.105 50.000 2.38 0.00 45.83 3.82
3549 5719 1.142667 TCCATGTGACCATGTGTGTGT 59.857 47.619 2.38 0.00 45.83 3.72
3550 5720 2.370189 TCCATGTGACCATGTGTGTGTA 59.630 45.455 2.38 0.00 45.83 2.90
3551 5721 3.145286 CCATGTGACCATGTGTGTGTAA 58.855 45.455 2.38 0.00 45.83 2.41
3552 5722 3.758023 CCATGTGACCATGTGTGTGTAAT 59.242 43.478 2.38 0.00 45.83 1.89
3553 5723 4.379708 CCATGTGACCATGTGTGTGTAATG 60.380 45.833 2.38 0.00 45.83 1.90
3554 5724 3.814625 TGTGACCATGTGTGTGTAATGT 58.185 40.909 0.00 0.00 0.00 2.71
3555 5725 3.563390 TGTGACCATGTGTGTGTAATGTG 59.437 43.478 0.00 0.00 0.00 3.21
3556 5726 3.563808 GTGACCATGTGTGTGTAATGTGT 59.436 43.478 0.00 0.00 0.00 3.72
3557 5727 4.036262 GTGACCATGTGTGTGTAATGTGTT 59.964 41.667 0.00 0.00 0.00 3.32
3558 5728 4.642437 TGACCATGTGTGTGTAATGTGTTT 59.358 37.500 0.00 0.00 0.00 2.83
3559 5729 5.181690 ACCATGTGTGTGTAATGTGTTTC 57.818 39.130 0.00 0.00 0.00 2.78
3560 5730 4.887071 ACCATGTGTGTGTAATGTGTTTCT 59.113 37.500 0.00 0.00 0.00 2.52
3561 5731 5.008613 ACCATGTGTGTGTAATGTGTTTCTC 59.991 40.000 0.00 0.00 0.00 2.87
3562 5732 5.008514 CCATGTGTGTGTAATGTGTTTCTCA 59.991 40.000 0.00 0.00 0.00 3.27
3563 5733 6.459435 CCATGTGTGTGTAATGTGTTTCTCAA 60.459 38.462 0.00 0.00 0.00 3.02
3564 5734 6.502136 TGTGTGTGTAATGTGTTTCTCAAA 57.498 33.333 0.00 0.00 0.00 2.69
3565 5735 6.914259 TGTGTGTGTAATGTGTTTCTCAAAA 58.086 32.000 0.00 0.00 0.00 2.44
3603 5798 3.257393 CGCTTTTGTGAGAGATGCTACT 58.743 45.455 0.00 0.00 0.00 2.57
3744 6336 8.693625 ACAACTTAGTACTACAATATCTCACCC 58.306 37.037 0.91 0.00 0.00 4.61
3745 6337 7.507733 ACTTAGTACTACAATATCTCACCCG 57.492 40.000 0.91 0.00 0.00 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
686 719 0.788391 GGACACAAACGTCCGATGTC 59.212 55.000 11.63 11.63 45.77 3.06
878 938 3.260884 CACCTAAAGTTACAGCTCAGGGA 59.739 47.826 0.00 0.00 0.00 4.20
947 1036 0.390998 GAGAGAGGAGTTGTGCTGGC 60.391 60.000 0.00 0.00 0.00 4.85
962 1051 3.545703 GTGAGAAGAGAGAGGGAGAGAG 58.454 54.545 0.00 0.00 0.00 3.20
964 1053 2.025416 TGGTGAGAAGAGAGAGGGAGAG 60.025 54.545 0.00 0.00 0.00 3.20
965 1054 1.996291 TGGTGAGAAGAGAGAGGGAGA 59.004 52.381 0.00 0.00 0.00 3.71
966 1055 2.378038 CTGGTGAGAAGAGAGAGGGAG 58.622 57.143 0.00 0.00 0.00 4.30
967 1056 1.006519 CCTGGTGAGAAGAGAGAGGGA 59.993 57.143 0.00 0.00 0.00 4.20
968 1057 1.006519 TCCTGGTGAGAAGAGAGAGGG 59.993 57.143 0.00 0.00 0.00 4.30
969 1058 2.523325 TCCTGGTGAGAAGAGAGAGG 57.477 55.000 0.00 0.00 0.00 3.69
1026 1116 5.009911 CAGAGAGAGAGAGAGAGAGAGAGAG 59.990 52.000 0.00 0.00 0.00 3.20
1027 1117 4.892345 CAGAGAGAGAGAGAGAGAGAGAGA 59.108 50.000 0.00 0.00 0.00 3.10
1028 1118 4.648762 ACAGAGAGAGAGAGAGAGAGAGAG 59.351 50.000 0.00 0.00 0.00 3.20
1029 1119 4.403752 CACAGAGAGAGAGAGAGAGAGAGA 59.596 50.000 0.00 0.00 0.00 3.10
1030 1120 4.161189 ACACAGAGAGAGAGAGAGAGAGAG 59.839 50.000 0.00 0.00 0.00 3.20
1031 1121 4.081476 CACACAGAGAGAGAGAGAGAGAGA 60.081 50.000 0.00 0.00 0.00 3.10
1032 1122 4.186926 CACACAGAGAGAGAGAGAGAGAG 58.813 52.174 0.00 0.00 0.00 3.20
1033 1123 3.582647 ACACACAGAGAGAGAGAGAGAGA 59.417 47.826 0.00 0.00 0.00 3.10
1081 1171 4.827087 ATCCTCAGCCACAGCGCG 62.827 66.667 0.00 0.00 46.67 6.86
1082 1172 3.200593 CATCCTCAGCCACAGCGC 61.201 66.667 0.00 0.00 46.67 5.92
1083 1173 1.376424 AACATCCTCAGCCACAGCG 60.376 57.895 0.00 0.00 46.67 5.18
1106 1214 4.157105 TCATCTGCCATTCAACAATCACAG 59.843 41.667 0.00 0.00 0.00 3.66
1201 1309 2.483876 TGAAGAACTTGGTCTTGCTCG 58.516 47.619 5.58 0.00 37.98 5.03
1289 1397 5.867716 AGTACAAGCGGTCAACTATTGTTAG 59.132 40.000 0.00 0.00 35.77 2.34
1337 1445 3.379452 TCCTTTTCTTTTTGCAAGGGGA 58.621 40.909 0.00 0.00 37.07 4.81
1344 1452 8.849490 GTTTTTCAAACATCCTTTTCTTTTTGC 58.151 29.630 0.00 0.00 0.00 3.68
1345 1453 9.890352 TGTTTTTCAAACATCCTTTTCTTTTTG 57.110 25.926 0.00 0.00 0.00 2.44
1363 1471 3.065648 GTCCTAGTTGCCGTTGTTTTTCA 59.934 43.478 0.00 0.00 0.00 2.69
1364 1472 3.314357 AGTCCTAGTTGCCGTTGTTTTTC 59.686 43.478 0.00 0.00 0.00 2.29
1419 1528 3.866651 ACATGACTGATGAGCCTTGTAC 58.133 45.455 0.00 0.00 35.80 2.90
1433 1542 7.382488 GCGTTTCTGATACATACATACATGACT 59.618 37.037 0.00 0.00 0.00 3.41
1444 1553 7.011016 CCATAAGTGTTGCGTTTCTGATACATA 59.989 37.037 0.00 0.00 0.00 2.29
1448 1560 5.121611 CACCATAAGTGTTGCGTTTCTGATA 59.878 40.000 0.00 0.00 41.93 2.15
1467 1579 7.392953 ACATTTTGTTTTTGGAGAAAACACCAT 59.607 29.630 14.51 8.39 46.14 3.55
1513 1626 5.727279 TGTACAGTCCATTATTGGGAGGTAA 59.273 40.000 3.86 0.00 43.81 2.85
1514 1627 5.282129 TGTACAGTCCATTATTGGGAGGTA 58.718 41.667 3.86 2.12 43.81 3.08
1515 1628 4.108570 TGTACAGTCCATTATTGGGAGGT 58.891 43.478 3.86 2.94 43.81 3.85
1516 1629 4.771114 TGTACAGTCCATTATTGGGAGG 57.229 45.455 3.86 0.00 43.81 4.30
1549 1662 3.612955 GCAGGCGATTAGTACAGAGGATC 60.613 52.174 0.00 0.00 0.00 3.36
1553 1666 1.409064 TGGCAGGCGATTAGTACAGAG 59.591 52.381 0.00 0.00 0.00 3.35
1556 1669 3.275617 AATTGGCAGGCGATTAGTACA 57.724 42.857 7.70 0.00 0.00 2.90
1557 1670 4.142469 ACAAAATTGGCAGGCGATTAGTAC 60.142 41.667 9.85 0.00 0.00 2.73
1558 1671 4.013728 ACAAAATTGGCAGGCGATTAGTA 58.986 39.130 9.85 0.00 0.00 1.82
1609 1749 3.777478 CCTGATGAAATTGCTCGCAAAT 58.223 40.909 8.54 0.00 39.55 2.32
1641 1781 0.405585 CAGGTCAAATCCCTGTGGGT 59.594 55.000 2.25 0.00 44.74 4.51
1667 1807 2.953821 CCATGTTTCGCCGCTTGT 59.046 55.556 0.00 0.00 0.00 3.16
1820 2003 3.255379 GCCGGTCGCATCGAAGAC 61.255 66.667 1.90 9.63 42.51 3.01
1849 2032 0.102120 CGCCAGCGAAGAGAGAAGAT 59.898 55.000 6.06 0.00 42.83 2.40
1873 2056 2.737783 ACCATGAAAATGTTTGCGCATG 59.262 40.909 12.75 1.39 34.47 4.06
1889 2072 2.368439 CTGTTGACCCACCATACCATG 58.632 52.381 0.00 0.00 0.00 3.66
1927 2110 8.265764 TCAGAATCAGAATCAGAATCATCACTT 58.734 33.333 0.00 0.00 0.00 3.16
1949 2144 1.064134 CGCCGTCGTCATCATCAGA 59.936 57.895 0.00 0.00 0.00 3.27
1950 2145 0.932123 CTCGCCGTCGTCATCATCAG 60.932 60.000 0.00 0.00 36.96 2.90
1965 2163 0.600557 ATCATCGTCATCCTCCTCGC 59.399 55.000 0.00 0.00 0.00 5.03
1967 2165 4.460731 TGTATCATCATCGTCATCCTCCTC 59.539 45.833 0.00 0.00 0.00 3.71
1968 2166 4.411013 TGTATCATCATCGTCATCCTCCT 58.589 43.478 0.00 0.00 0.00 3.69
1969 2167 4.790765 TGTATCATCATCGTCATCCTCC 57.209 45.455 0.00 0.00 0.00 4.30
1970 2168 5.632764 CACTTGTATCATCATCGTCATCCTC 59.367 44.000 0.00 0.00 0.00 3.71
1971 2169 5.069648 ACACTTGTATCATCATCGTCATCCT 59.930 40.000 0.00 0.00 0.00 3.24
1972 2170 5.176406 CACACTTGTATCATCATCGTCATCC 59.824 44.000 0.00 0.00 0.00 3.51
1973 2171 5.332883 GCACACTTGTATCATCATCGTCATC 60.333 44.000 0.00 0.00 0.00 2.92
1974 2172 4.509230 GCACACTTGTATCATCATCGTCAT 59.491 41.667 0.00 0.00 0.00 3.06
1975 2173 3.865164 GCACACTTGTATCATCATCGTCA 59.135 43.478 0.00 0.00 0.00 4.35
1976 2174 3.246226 GGCACACTTGTATCATCATCGTC 59.754 47.826 0.00 0.00 0.00 4.20
1977 2175 3.198068 GGCACACTTGTATCATCATCGT 58.802 45.455 0.00 0.00 0.00 3.73
1978 2176 2.219445 CGGCACACTTGTATCATCATCG 59.781 50.000 0.00 0.00 0.00 3.84
1979 2177 3.001634 CACGGCACACTTGTATCATCATC 59.998 47.826 0.00 0.00 0.00 2.92
2001 2199 0.247736 ACGGGACTCAATCAGCTGAC 59.752 55.000 20.97 4.72 0.00 3.51
2006 2204 3.193263 CATTCTGACGGGACTCAATCAG 58.807 50.000 0.00 0.00 39.99 2.90
2056 2254 3.571590 TGATGCCTTACTTGGTTTGGTT 58.428 40.909 0.00 0.00 0.00 3.67
2076 2281 3.622612 TCATGCATTAGTCGAACCACATG 59.377 43.478 0.00 0.00 35.99 3.21
2115 2326 6.054295 CACCAAGATCTCAAGAAAGGGATAG 58.946 44.000 0.00 0.00 0.00 2.08
2310 2591 2.750166 GTCGTCATCACTCTCCTCTTCA 59.250 50.000 0.00 0.00 0.00 3.02
2328 2609 2.531912 GTCGAAGTCAGCATATGTGTCG 59.468 50.000 4.29 7.31 0.00 4.35
2370 2651 0.665369 CGTCGTCGGGTAGTTGCTTT 60.665 55.000 0.00 0.00 0.00 3.51
2548 2829 0.239347 GTGCATGCCAGAGTTGACAC 59.761 55.000 16.68 0.00 0.00 3.67
2629 3045 7.022055 TGTGAAGATGTTCGTGTACAAATTT 57.978 32.000 0.00 0.00 35.17 1.82
2825 3244 1.208052 CCGCCTTCTTCTCATTCCTCA 59.792 52.381 0.00 0.00 0.00 3.86
2843 3265 3.872728 TCATCGTCGTCCTCGCCG 61.873 66.667 0.00 0.00 39.77 6.46
2885 3307 2.900167 GCAAACCGACCGTTGGACC 61.900 63.158 12.15 0.00 33.93 4.46
2934 3358 1.135141 TGCCAAAATATTCAGCGCACC 60.135 47.619 11.47 0.00 0.00 5.01
3051 3479 2.044793 TCAGTGGTGATTTCCCCTCT 57.955 50.000 0.00 0.00 0.00 3.69
3081 3512 3.423154 GGGTGCAGCGGAAAGACG 61.423 66.667 10.24 0.00 0.00 4.18
3095 3526 2.293184 ACTAGTCACATCTCATGGGGGT 60.293 50.000 0.00 0.00 33.47 4.95
3112 3543 3.118956 CCTTAGTCTTGGAGGTGCACTAG 60.119 52.174 17.98 6.93 0.00 2.57
3151 3582 7.907214 AACACAAAGACAGATCTTACCATAC 57.093 36.000 0.00 0.00 44.82 2.39
3270 3707 2.607635 GAGCATTGCAAAAGCATGATGG 59.392 45.455 23.69 0.00 44.18 3.51
3378 5541 7.225538 GCATCATGTTATATAGGCAGTACATCC 59.774 40.741 0.00 0.00 0.00 3.51
3455 5619 9.170734 AGACACATAAATATAAGCATAGGCATG 57.829 33.333 0.67 0.00 44.61 4.06
3496 5664 4.214310 ACTCACATCATCCAACCACAAAA 58.786 39.130 0.00 0.00 0.00 2.44
3497 5665 3.831323 ACTCACATCATCCAACCACAAA 58.169 40.909 0.00 0.00 0.00 2.83
3537 5707 4.887071 AGAAACACATTACACACACATGGT 59.113 37.500 0.00 0.00 0.00 3.55
3538 5708 5.008514 TGAGAAACACATTACACACACATGG 59.991 40.000 0.00 0.00 0.00 3.66
3539 5709 6.058827 TGAGAAACACATTACACACACATG 57.941 37.500 0.00 0.00 0.00 3.21
3540 5710 6.691754 TTGAGAAACACATTACACACACAT 57.308 33.333 0.00 0.00 0.00 3.21
3541 5711 6.502136 TTTGAGAAACACATTACACACACA 57.498 33.333 0.00 0.00 0.00 3.72
3542 5712 7.753132 TCTTTTTGAGAAACACATTACACACAC 59.247 33.333 0.00 0.00 0.00 3.82
3543 5713 7.821652 TCTTTTTGAGAAACACATTACACACA 58.178 30.769 0.00 0.00 0.00 3.72
3544 5714 8.682128 TTCTTTTTGAGAAACACATTACACAC 57.318 30.769 0.00 0.00 41.34 3.82
3603 5798 5.277250 TGGACCAGGTTCATAGAATCACTA 58.723 41.667 0.00 0.00 35.42 2.74
3663 5858 5.163416 ACAAAAACACAAGGAAATGAGAGGG 60.163 40.000 0.00 0.00 0.00 4.30
3868 6460 8.908786 AGAATTAACACTCAAGACTTCATCAA 57.091 30.769 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.