Multiple sequence alignment - TraesCS4D01G195200

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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 TraesCS4D01G195200 chr4D 100.000 3605 0 0 1 3605 338839417 338835813 0.000000e+00 6658.0
1 TraesCS4D01G195200 chr4D 90.164 61 4 2 3086 3144 494042418 494042478 1.070000e-10 78.7
2 TraesCS4D01G195200 chr4B 88.408 2424 116 55 332 2689 417772197 417769873 0.000000e+00 2767.0
3 TraesCS4D01G195200 chr4B 89.720 749 63 9 2863 3605 417769869 417769129 0.000000e+00 944.0
4 TraesCS4D01G195200 chr4A 89.808 1982 88 46 1 1946 133369965 133371868 0.000000e+00 2436.0
5 TraesCS4D01G195200 chr4A 91.487 1069 60 15 1975 3033 133371867 133372914 0.000000e+00 1441.0
6 TraesCS4D01G195200 chr4A 96.000 50 2 0 3090 3139 121501276 121501325 8.300000e-12 82.4
7 TraesCS4D01G195200 chr7B 83.401 247 14 12 1012 1258 336466143 336465924 1.700000e-48 204.0
8 TraesCS4D01G195200 chr7B 94.737 57 3 0 3082 3138 748588410 748588466 4.960000e-14 89.8
9 TraesCS4D01G195200 chr2A 96.078 51 2 0 3086 3136 74972559 74972509 2.310000e-12 84.2
10 TraesCS4D01G195200 chr2D 91.803 61 2 3 3090 3148 116513264 116513205 8.300000e-12 82.4
11 TraesCS4D01G195200 chr5D 90.164 61 4 2 3077 3136 285024172 285024113 1.070000e-10 78.7
12 TraesCS4D01G195200 chrUn 88.710 62 4 3 3077 3136 20829141 20829081 4.990000e-09 73.1
13 TraesCS4D01G195200 chr3A 88.710 62 4 2 3086 3146 567538329 567538388 4.990000e-09 73.1


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 TraesCS4D01G195200 chr4D 338835813 338839417 3604 True 6658.0 6658 100.0000 1 3605 1 chr4D.!!$R1 3604
1 TraesCS4D01G195200 chr4B 417769129 417772197 3068 True 1855.5 2767 89.0640 332 3605 2 chr4B.!!$R1 3273
2 TraesCS4D01G195200 chr4A 133369965 133372914 2949 False 1938.5 2436 90.6475 1 3033 2 chr4A.!!$F2 3032

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
765 814 0.179004 AAACCCCTGCATCACGTGAA 60.179 50.0 24.13 5.15 0.0 3.18 F
1339 1420 0.110056 CACAAACTGCGCCATGACTC 60.110 55.0 4.18 0.00 0.0 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1959 2077 0.036483 ACACAGCACACACAGTCACA 60.036 50.0 0.00 0.0 0.0 3.58 R
2747 2873 0.179468 ACGTGTGGGCTACTGTTTGT 59.821 50.0 1.79 0.0 0.0 2.83 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
144 145 3.486383 CAAAAGTCACAGCCTTTAGGGA 58.514 45.455 0.00 0.00 37.23 4.20
184 185 5.471456 GGCATGAAACGGAGAATCAAGATAT 59.529 40.000 0.00 0.00 36.25 1.63
214 215 9.804547 CGTCTCTTTAATTCTCAAAAGAAAGAG 57.195 33.333 13.48 13.48 44.49 2.85
242 248 6.228273 TCTCAAAAGAAATACACAAGAGCG 57.772 37.500 0.00 0.00 0.00 5.03
268 274 6.409704 GTTAACCGAGGGAGGTAAAATTACT 58.590 40.000 0.00 0.00 45.21 2.24
324 330 2.434702 AGTCGTTCTTCTGTTCCTTGGT 59.565 45.455 0.00 0.00 0.00 3.67
325 331 3.118371 AGTCGTTCTTCTGTTCCTTGGTT 60.118 43.478 0.00 0.00 0.00 3.67
326 332 3.626217 GTCGTTCTTCTGTTCCTTGGTTT 59.374 43.478 0.00 0.00 0.00 3.27
327 333 4.095932 GTCGTTCTTCTGTTCCTTGGTTTT 59.904 41.667 0.00 0.00 0.00 2.43
328 334 4.703093 TCGTTCTTCTGTTCCTTGGTTTTT 59.297 37.500 0.00 0.00 0.00 1.94
415 421 1.319541 GGCAGCCACTAGACTATCGA 58.680 55.000 6.55 0.00 0.00 3.59
505 533 0.530744 TCGCTGCCTCAAATAGACGT 59.469 50.000 0.00 0.00 0.00 4.34
506 534 1.067142 TCGCTGCCTCAAATAGACGTT 60.067 47.619 0.00 0.00 0.00 3.99
611 641 5.591099 ACATAAACATTCCATTTCGATGCC 58.409 37.500 0.00 0.00 0.00 4.40
705 736 6.477688 GCAACAACAAATCCATAGATTCCATG 59.522 38.462 0.00 0.00 42.03 3.66
708 739 6.097270 ACAACAAATCCATAGATTCCATGGTG 59.903 38.462 12.58 0.71 42.03 4.17
709 740 5.769835 ACAAATCCATAGATTCCATGGTGT 58.230 37.500 12.58 5.73 42.03 4.16
725 756 2.359975 GTGTAGTGCCCCACTGCC 60.360 66.667 8.06 0.10 44.36 4.85
741 790 1.524355 CTGCCAATGCTAAGACGATCG 59.476 52.381 14.88 14.88 38.71 3.69
742 791 1.134818 TGCCAATGCTAAGACGATCGT 60.135 47.619 22.97 22.97 38.71 3.73
743 792 1.523095 GCCAATGCTAAGACGATCGTC 59.477 52.381 35.26 35.26 38.80 4.20
744 793 3.971824 GCCAATGCTAAGACGATCGTCG 61.972 54.545 35.21 24.88 41.28 5.12
751 800 3.078560 GACGATCGTCGCAAACCC 58.921 61.111 30.46 8.01 45.12 4.11
752 801 2.433664 ACGATCGTCGCAAACCCC 60.434 61.111 16.60 0.00 45.12 4.95
753 802 2.125673 CGATCGTCGCAAACCCCT 60.126 61.111 7.03 0.00 31.14 4.79
754 803 2.452813 CGATCGTCGCAAACCCCTG 61.453 63.158 7.03 0.00 31.14 4.45
755 804 2.746277 ATCGTCGCAAACCCCTGC 60.746 61.111 0.00 0.00 39.04 4.85
756 805 3.545124 ATCGTCGCAAACCCCTGCA 62.545 57.895 0.00 0.00 42.77 4.41
757 806 2.819984 ATCGTCGCAAACCCCTGCAT 62.820 55.000 0.00 0.00 42.77 3.96
758 807 2.877691 GTCGCAAACCCCTGCATC 59.122 61.111 0.00 0.00 42.77 3.91
759 808 1.971167 GTCGCAAACCCCTGCATCA 60.971 57.895 0.00 0.00 42.77 3.07
760 809 1.971167 TCGCAAACCCCTGCATCAC 60.971 57.895 0.00 0.00 42.77 3.06
761 810 2.568090 GCAAACCCCTGCATCACG 59.432 61.111 0.00 0.00 42.17 4.35
762 811 2.268076 GCAAACCCCTGCATCACGT 61.268 57.895 0.00 0.00 42.17 4.49
763 812 1.580942 CAAACCCCTGCATCACGTG 59.419 57.895 9.94 9.94 0.00 4.49
764 813 0.888736 CAAACCCCTGCATCACGTGA 60.889 55.000 22.48 22.48 0.00 4.35
765 814 0.179004 AAACCCCTGCATCACGTGAA 60.179 50.000 24.13 5.15 0.00 3.18
766 815 0.889186 AACCCCTGCATCACGTGAAC 60.889 55.000 24.13 17.96 0.00 3.18
767 816 1.003355 CCCCTGCATCACGTGAACT 60.003 57.895 24.13 3.63 0.00 3.01
768 817 1.300971 CCCCTGCATCACGTGAACTG 61.301 60.000 24.13 18.19 0.00 3.16
769 818 0.603707 CCCTGCATCACGTGAACTGT 60.604 55.000 24.13 2.30 0.00 3.55
770 819 1.337728 CCCTGCATCACGTGAACTGTA 60.338 52.381 24.13 15.51 0.00 2.74
771 820 2.412870 CCTGCATCACGTGAACTGTAA 58.587 47.619 24.13 9.07 0.00 2.41
772 821 3.002791 CCTGCATCACGTGAACTGTAAT 58.997 45.455 24.13 0.11 0.00 1.89
773 822 3.062639 CCTGCATCACGTGAACTGTAATC 59.937 47.826 24.13 5.07 0.00 1.75
774 823 2.666022 TGCATCACGTGAACTGTAATCG 59.334 45.455 24.13 3.93 0.00 3.34
775 824 2.029244 GCATCACGTGAACTGTAATCGG 59.971 50.000 24.13 3.47 0.00 4.18
776 825 1.705256 TCACGTGAACTGTAATCGGC 58.295 50.000 17.62 0.00 0.00 5.54
779 828 1.418342 CGTGAACTGTAATCGGCCGG 61.418 60.000 27.83 10.66 0.00 6.13
861 915 8.417780 AATAATTCTCTCTTCATTCAGTCACG 57.582 34.615 0.00 0.00 0.00 4.35
862 916 5.651387 ATTCTCTCTTCATTCAGTCACGA 57.349 39.130 0.00 0.00 0.00 4.35
873 927 2.502080 GTCACGACTCACGAGCCG 60.502 66.667 0.96 0.96 45.77 5.52
874 928 4.400109 TCACGACTCACGAGCCGC 62.400 66.667 2.49 0.00 45.77 6.53
928 996 0.657659 CTCGTGATCGATTCGTCGGG 60.658 60.000 18.32 9.71 45.21 5.14
1050 1118 4.459089 GTCCTGCTCCTCCACGCC 62.459 72.222 0.00 0.00 0.00 5.68
1056 1124 2.043450 CTCCTCCACGCCCTCTCT 60.043 66.667 0.00 0.00 0.00 3.10
1322 1403 2.486128 CGTACGTACGTGACTGTACAC 58.514 52.381 33.95 16.29 43.89 2.90
1336 1417 0.871722 GTACACAAACTGCGCCATGA 59.128 50.000 4.18 0.00 0.00 3.07
1337 1418 0.871722 TACACAAACTGCGCCATGAC 59.128 50.000 4.18 0.00 0.00 3.06
1338 1419 0.819259 ACACAAACTGCGCCATGACT 60.819 50.000 4.18 0.00 0.00 3.41
1339 1420 0.110056 CACAAACTGCGCCATGACTC 60.110 55.000 4.18 0.00 0.00 3.36
1340 1421 0.534877 ACAAACTGCGCCATGACTCA 60.535 50.000 4.18 0.00 0.00 3.41
1341 1422 0.806868 CAAACTGCGCCATGACTCAT 59.193 50.000 4.18 0.00 0.00 2.90
1342 1423 0.806868 AAACTGCGCCATGACTCATG 59.193 50.000 11.59 11.59 41.10 3.07
1352 1433 2.371306 CATGACTCATGGTGATTGCCA 58.629 47.619 10.79 0.00 43.48 4.92
1360 1441 0.959867 TGGTGATTGCCATGGTCGTG 60.960 55.000 14.67 0.00 32.81 4.35
1437 1522 2.139888 TACGTAGGTTTGACGGCGCA 62.140 55.000 10.83 2.81 44.58 6.09
1485 1570 1.607612 GGTGATGTTCGTGGGGGAT 59.392 57.895 0.00 0.00 0.00 3.85
1581 1666 1.228306 CTCCGCCGACCCTCTCTAT 60.228 63.158 0.00 0.00 0.00 1.98
1604 1693 2.268298 CTACAGGTTCATGGTACGTGC 58.732 52.381 16.33 0.00 35.42 5.34
1610 1699 0.738063 TTCATGGTACGTGCGCGATT 60.738 50.000 28.73 7.43 42.00 3.34
1626 1715 1.333169 CGATTCATGCACATACACGCC 60.333 52.381 0.00 0.00 0.00 5.68
1639 1742 2.225068 ACACGCCCTCGATATTCTTG 57.775 50.000 0.00 0.00 39.41 3.02
1640 1743 0.861837 CACGCCCTCGATATTCTTGC 59.138 55.000 0.00 0.00 39.41 4.01
1645 1748 2.545946 GCCCTCGATATTCTTGCTGTTC 59.454 50.000 0.00 0.00 0.00 3.18
1648 1752 2.797156 CTCGATATTCTTGCTGTTCGGG 59.203 50.000 0.00 0.00 0.00 5.14
1661 1765 0.599060 GTTCGGGAATTTGGGCGAAA 59.401 50.000 0.00 0.00 0.00 3.46
1665 1769 3.090037 TCGGGAATTTGGGCGAAATTAA 58.910 40.909 18.32 4.40 43.12 1.40
1666 1770 3.119424 TCGGGAATTTGGGCGAAATTAAC 60.119 43.478 18.32 14.22 43.12 2.01
1667 1771 3.119280 CGGGAATTTGGGCGAAATTAACT 60.119 43.478 18.32 0.00 43.12 2.24
1671 1775 6.391537 GGAATTTGGGCGAAATTAACTACAA 58.608 36.000 18.32 0.00 43.12 2.41
1673 1777 6.584185 ATTTGGGCGAAATTAACTACAACT 57.416 33.333 1.26 0.00 29.22 3.16
1674 1778 7.690952 ATTTGGGCGAAATTAACTACAACTA 57.309 32.000 1.26 0.00 29.22 2.24
1676 1780 5.797051 TGGGCGAAATTAACTACAACTACT 58.203 37.500 0.00 0.00 0.00 2.57
1678 1782 6.148150 TGGGCGAAATTAACTACAACTACTTG 59.852 38.462 0.00 0.00 0.00 3.16
1691 1809 1.829222 ACTACTTGGACATGTACCGGG 59.171 52.381 6.32 5.46 0.00 5.73
1693 1811 1.451387 CTTGGACATGTACCGGGCC 60.451 63.158 6.32 0.00 0.00 5.80
1775 1893 2.669240 CAGGGGAAACGGGTCCTC 59.331 66.667 6.60 2.68 38.61 3.71
1901 2019 2.791501 TACGCCCGCCCAGTTTCTTC 62.792 60.000 0.00 0.00 0.00 2.87
1927 2045 2.414138 CCAGTTTAGCTTCGTTTACCGG 59.586 50.000 0.00 0.00 37.11 5.28
1965 2083 3.289128 CACCATCGTGTGTGTGACT 57.711 52.632 0.00 0.00 35.10 3.41
1966 2084 0.861185 CACCATCGTGTGTGTGACTG 59.139 55.000 0.00 0.00 35.10 3.51
1967 2085 0.464036 ACCATCGTGTGTGTGACTGT 59.536 50.000 0.00 0.00 0.00 3.55
1968 2086 0.861185 CCATCGTGTGTGTGACTGTG 59.139 55.000 0.00 0.00 0.00 3.66
1969 2087 1.570813 CATCGTGTGTGTGACTGTGT 58.429 50.000 0.00 0.00 0.00 3.72
1970 2088 1.258720 CATCGTGTGTGTGACTGTGTG 59.741 52.381 0.00 0.00 0.00 3.82
1971 2089 0.245266 TCGTGTGTGTGACTGTGTGT 59.755 50.000 0.00 0.00 0.00 3.72
1972 2090 0.369931 CGTGTGTGTGACTGTGTGTG 59.630 55.000 0.00 0.00 0.00 3.82
1973 2091 0.096976 GTGTGTGTGACTGTGTGTGC 59.903 55.000 0.00 0.00 0.00 4.57
1974 2092 0.036483 TGTGTGTGACTGTGTGTGCT 60.036 50.000 0.00 0.00 0.00 4.40
1975 2093 0.374758 GTGTGTGACTGTGTGTGCTG 59.625 55.000 0.00 0.00 0.00 4.41
2029 2147 2.812983 CGGTACTCGGAGGACATGGATA 60.813 54.545 21.41 0.00 34.75 2.59
2176 2294 0.538584 CTCTGCACTGCACCCATCTA 59.461 55.000 0.00 0.00 33.79 1.98
2213 2331 3.262420 CTCACACCCTGTATTACACTGC 58.738 50.000 0.00 0.00 0.00 4.40
2217 2335 3.002791 CACCCTGTATTACACTGCACTG 58.997 50.000 0.00 0.00 0.00 3.66
2224 2342 7.094377 CCCTGTATTACACTGCACTGTATTTTT 60.094 37.037 6.99 0.00 0.00 1.94
2322 2442 1.000506 GTGTCCAAGAACTGCTACGGA 59.999 52.381 0.00 0.00 0.00 4.69
2338 2458 1.522569 GGAGAGACGGTCCCATTGG 59.477 63.158 4.14 0.00 0.00 3.16
2633 2758 1.304381 GGACCTGCATTTGGCCAGA 60.304 57.895 5.11 0.08 43.89 3.86
2642 2767 1.956629 ATTTGGCCAGATGCTGCAGC 61.957 55.000 31.89 31.89 40.92 5.25
2708 2834 2.100916 GTGTCATGTGAGCGGTATAGGT 59.899 50.000 0.00 0.00 0.00 3.08
2723 2849 6.350194 GCGGTATAGGTAGACATGATTGATGA 60.350 42.308 0.00 0.00 35.80 2.92
2747 2873 8.048514 TGAGGATGTACATTGATCTTTGAATGA 58.951 33.333 10.30 0.00 34.31 2.57
2754 2880 9.121517 GTACATTGATCTTTGAATGACAAACAG 57.878 33.333 9.74 0.00 42.57 3.16
2755 2881 7.719483 ACATTGATCTTTGAATGACAAACAGT 58.281 30.769 9.74 0.00 42.57 3.55
2759 2885 5.689383 TCTTTGAATGACAAACAGTAGCC 57.311 39.130 0.00 0.00 42.57 3.93
2765 2891 0.865769 GACAAACAGTAGCCCACACG 59.134 55.000 0.00 0.00 0.00 4.49
2766 2892 0.179468 ACAAACAGTAGCCCACACGT 59.821 50.000 0.00 0.00 0.00 4.49
2774 2900 3.370978 CAGTAGCCCACACGTTTGATTAG 59.629 47.826 2.58 0.00 0.00 1.73
2790 2916 7.165812 CGTTTGATTAGTAATAGCAAACATGCC 59.834 37.037 25.03 10.19 45.04 4.40
2792 2918 5.238432 TGATTAGTAATAGCAAACATGCCCG 59.762 40.000 0.00 0.00 34.90 6.13
2794 2920 4.145365 AGTAATAGCAAACATGCCCGTA 57.855 40.909 0.00 0.00 34.90 4.02
2795 2921 3.875134 AGTAATAGCAAACATGCCCGTAC 59.125 43.478 0.00 0.00 34.90 3.67
2799 2925 0.039888 GCAAACATGCCCGTACGTTT 60.040 50.000 15.21 3.98 31.96 3.60
2800 2926 1.680668 CAAACATGCCCGTACGTTTG 58.319 50.000 15.21 12.69 41.39 2.93
2801 2927 0.039888 AAACATGCCCGTACGTTTGC 60.040 50.000 15.21 13.87 30.70 3.68
2803 2929 1.167155 ACATGCCCGTACGTTTGCAA 61.167 50.000 22.42 0.00 37.27 4.08
2804 2930 0.727793 CATGCCCGTACGTTTGCAAC 60.728 55.000 22.42 0.00 37.27 4.17
2839 2966 6.839124 ACCATGTGCTTAAAATTCATGAGA 57.161 33.333 0.00 0.00 38.35 3.27
3013 3142 1.670811 CCATAGACCGCAATCCAACAC 59.329 52.381 0.00 0.00 0.00 3.32
3021 3150 0.804364 GCAATCCAACACGCATCTCA 59.196 50.000 0.00 0.00 0.00 3.27
3027 3156 4.582701 TCCAACACGCATCTCAAAAATT 57.417 36.364 0.00 0.00 0.00 1.82
3035 3164 5.865552 CACGCATCTCAAAAATTTCCTCAAT 59.134 36.000 0.00 0.00 0.00 2.57
3044 3173 8.248904 TCAAAAATTTCCTCAATCTTTCTCCA 57.751 30.769 0.00 0.00 0.00 3.86
3058 3187 2.692709 TCTCCAAAGAAATTGCCCCA 57.307 45.000 0.00 0.00 37.73 4.96
3062 3191 3.831911 CTCCAAAGAAATTGCCCCAAGTA 59.168 43.478 0.00 0.00 37.73 2.24
3090 3219 0.970937 CTTGCACTCCCTCCGTCCTA 60.971 60.000 0.00 0.00 0.00 2.94
3096 3225 3.094572 CACTCCCTCCGTCCTAAAGTTA 58.905 50.000 0.00 0.00 0.00 2.24
3098 3227 3.245550 ACTCCCTCCGTCCTAAAGTTAGT 60.246 47.826 0.00 0.00 0.00 2.24
3145 3274 7.355101 TGAGACAGAGGGACTACATAACTAAT 58.645 38.462 0.00 0.00 41.55 1.73
3162 3291 9.651913 CATAACTAATTTTGCACAAATAAGGGT 57.348 29.630 0.00 3.73 0.00 4.34
3163 3292 9.869757 ATAACTAATTTTGCACAAATAAGGGTC 57.130 29.630 0.00 0.00 0.00 4.46
3164 3293 6.697395 ACTAATTTTGCACAAATAAGGGTCC 58.303 36.000 0.00 0.00 0.00 4.46
3165 3294 5.559148 AATTTTGCACAAATAAGGGTCCA 57.441 34.783 0.00 0.00 0.00 4.02
3166 3295 5.760484 ATTTTGCACAAATAAGGGTCCAT 57.240 34.783 0.00 0.00 0.00 3.41
3167 3296 4.799564 TTTGCACAAATAAGGGTCCATC 57.200 40.909 0.00 0.00 0.00 3.51
3175 3305 6.153340 CACAAATAAGGGTCCATCAGTCAAAT 59.847 38.462 0.00 0.00 0.00 2.32
3197 3327 5.810080 TTTTGACGGGGGAAATATTTTGT 57.190 34.783 1.43 0.00 0.00 2.83
3201 3331 4.701171 TGACGGGGGAAATATTTTGTACAC 59.299 41.667 1.43 0.00 0.00 2.90
3223 3353 7.234355 ACACAGGAAAATCTATCCAAAGAACT 58.766 34.615 0.00 0.00 39.55 3.01
3224 3354 7.175641 ACACAGGAAAATCTATCCAAAGAACTG 59.824 37.037 0.00 0.00 39.55 3.16
3229 3359 7.757173 GGAAAATCTATCCAAAGAACTGCTTTC 59.243 37.037 0.00 0.00 44.83 2.62
3231 3361 5.147330 TCTATCCAAAGAACTGCTTTCGA 57.853 39.130 0.00 0.00 44.83 3.71
3269 3399 9.790389 AAACATCACTAGTAGAACTAAAGATCG 57.210 33.333 3.59 0.00 29.00 3.69
3276 3406 7.975058 ACTAGTAGAACTAAAGATCGCCTTTTC 59.025 37.037 3.59 1.71 42.13 2.29
3288 3418 0.540597 GCCTTTTCAGGGGAAGCACT 60.541 55.000 0.00 0.00 41.21 4.40
3289 3419 1.271926 GCCTTTTCAGGGGAAGCACTA 60.272 52.381 0.00 0.00 41.21 2.74
3290 3420 2.817839 GCCTTTTCAGGGGAAGCACTAA 60.818 50.000 0.00 0.00 41.21 2.24
3291 3421 3.496331 CCTTTTCAGGGGAAGCACTAAA 58.504 45.455 0.00 0.00 36.36 1.85
3292 3422 4.089361 CCTTTTCAGGGGAAGCACTAAAT 58.911 43.478 0.00 0.00 36.36 1.40
3300 3430 7.867921 TCAGGGGAAGCACTAAATTAAAGATA 58.132 34.615 0.00 0.00 0.00 1.98
3324 3454 7.739498 ATACTAACAACGAATCAACCACTTT 57.261 32.000 0.00 0.00 0.00 2.66
3337 3467 0.105408 CCACTTTGGCAAGCAAGCTT 59.895 50.000 0.59 0.59 36.60 3.74
3371 3501 2.227388 GGAGTCGAACCTGTAGACGAAA 59.773 50.000 0.00 0.00 39.65 3.46
3411 3541 8.688747 TTTCATTATTTTGGGAAACAGCAAAT 57.311 26.923 0.00 0.00 0.00 2.32
3412 3542 7.903995 TCATTATTTTGGGAAACAGCAAATC 57.096 32.000 0.00 0.00 0.00 2.17
3421 3551 5.357878 TGGGAAACAGCAAATCTATGATCAC 59.642 40.000 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
170 171 4.636249 AGACGGCAATATCTTGATTCTCC 58.364 43.478 0.00 0.00 34.04 3.71
184 185 6.485313 TCTTTTGAGAATTAAAGAGACGGCAA 59.515 34.615 0.00 0.00 35.93 4.52
217 218 7.301054 CGCTCTTGTGTATTTCTTTTGAGAAT 58.699 34.615 0.00 0.00 0.00 2.40
220 221 5.385617 CCGCTCTTGTGTATTTCTTTTGAG 58.614 41.667 0.00 0.00 0.00 3.02
221 222 4.215399 CCCGCTCTTGTGTATTTCTTTTGA 59.785 41.667 0.00 0.00 0.00 2.69
224 225 3.751518 ACCCGCTCTTGTGTATTTCTTT 58.248 40.909 0.00 0.00 0.00 2.52
225 226 3.418684 ACCCGCTCTTGTGTATTTCTT 57.581 42.857 0.00 0.00 0.00 2.52
226 227 3.418684 AACCCGCTCTTGTGTATTTCT 57.581 42.857 0.00 0.00 0.00 2.52
227 228 4.142752 GGTTAACCCGCTCTTGTGTATTTC 60.143 45.833 14.16 0.00 0.00 2.17
228 229 3.754850 GGTTAACCCGCTCTTGTGTATTT 59.245 43.478 14.16 0.00 0.00 1.40
229 230 3.340928 GGTTAACCCGCTCTTGTGTATT 58.659 45.455 14.16 0.00 0.00 1.89
230 231 2.981898 GGTTAACCCGCTCTTGTGTAT 58.018 47.619 14.16 0.00 0.00 2.29
242 248 1.571955 TTACCTCCCTCGGTTAACCC 58.428 55.000 19.09 1.64 38.49 4.11
268 274 1.751924 GTTTTGGCACCAGTAACCACA 59.248 47.619 0.00 0.00 31.83 4.17
326 332 3.550639 CCGCATGCACTTCAAGAGAAAAA 60.551 43.478 19.57 0.00 32.35 1.94
327 333 2.030893 CCGCATGCACTTCAAGAGAAAA 60.031 45.455 19.57 0.00 32.35 2.29
328 334 1.536766 CCGCATGCACTTCAAGAGAAA 59.463 47.619 19.57 0.00 32.35 2.52
329 335 1.159285 CCGCATGCACTTCAAGAGAA 58.841 50.000 19.57 0.00 0.00 2.87
330 336 1.300971 GCCGCATGCACTTCAAGAGA 61.301 55.000 19.57 0.00 40.77 3.10
415 421 1.690985 GGCCAAGCTAGTCCCCTCT 60.691 63.158 0.00 0.00 0.00 3.69
505 533 7.964666 TTTCTTACCTTTCCTTCCTTTTCAA 57.035 32.000 0.00 0.00 0.00 2.69
506 534 7.964666 TTTTCTTACCTTTCCTTCCTTTTCA 57.035 32.000 0.00 0.00 0.00 2.69
611 641 1.265635 TGAGTTTTGGAATTCGTGCGG 59.734 47.619 0.00 0.00 0.00 5.69
705 736 1.302511 CAGTGGGGCACTACACACC 60.303 63.158 4.86 0.00 43.43 4.16
708 739 2.359975 GGCAGTGGGGCACTACAC 60.360 66.667 4.86 0.00 43.43 2.90
725 756 1.188138 GCGACGATCGTCTTAGCATTG 59.812 52.381 37.12 23.57 42.81 2.82
744 793 2.268076 ACGTGATGCAGGGGTTTGC 61.268 57.895 0.00 0.00 44.33 3.68
745 794 0.888736 TCACGTGATGCAGGGGTTTG 60.889 55.000 15.76 0.00 0.00 2.93
746 795 0.179004 TTCACGTGATGCAGGGGTTT 60.179 50.000 20.80 0.00 0.00 3.27
747 796 0.889186 GTTCACGTGATGCAGGGGTT 60.889 55.000 20.80 0.00 0.00 4.11
748 797 1.302511 GTTCACGTGATGCAGGGGT 60.303 57.895 20.80 0.00 0.00 4.95
749 798 1.003355 AGTTCACGTGATGCAGGGG 60.003 57.895 20.80 0.00 0.00 4.79
750 799 0.603707 ACAGTTCACGTGATGCAGGG 60.604 55.000 20.80 8.64 0.00 4.45
751 800 2.078849 TACAGTTCACGTGATGCAGG 57.921 50.000 20.80 13.34 0.00 4.85
752 801 3.241773 CGATTACAGTTCACGTGATGCAG 60.242 47.826 20.80 14.23 0.00 4.41
753 802 2.666022 CGATTACAGTTCACGTGATGCA 59.334 45.455 20.80 3.26 0.00 3.96
754 803 2.029244 CCGATTACAGTTCACGTGATGC 59.971 50.000 20.80 15.21 0.00 3.91
755 804 2.029244 GCCGATTACAGTTCACGTGATG 59.971 50.000 20.80 17.93 0.00 3.07
756 805 2.268298 GCCGATTACAGTTCACGTGAT 58.732 47.619 20.80 6.87 0.00 3.06
757 806 1.670674 GGCCGATTACAGTTCACGTGA 60.671 52.381 15.76 15.76 0.00 4.35
758 807 0.719465 GGCCGATTACAGTTCACGTG 59.281 55.000 9.94 9.94 0.00 4.49
759 808 0.734942 CGGCCGATTACAGTTCACGT 60.735 55.000 24.07 0.00 0.00 4.49
760 809 1.418342 CCGGCCGATTACAGTTCACG 61.418 60.000 30.73 0.00 0.00 4.35
761 810 1.702491 GCCGGCCGATTACAGTTCAC 61.702 60.000 30.73 0.00 0.00 3.18
762 811 1.448893 GCCGGCCGATTACAGTTCA 60.449 57.895 30.73 0.00 0.00 3.18
763 812 1.022451 TTGCCGGCCGATTACAGTTC 61.022 55.000 30.73 4.15 0.00 3.01
764 813 1.003112 TTGCCGGCCGATTACAGTT 60.003 52.632 30.73 0.00 0.00 3.16
765 814 1.743995 GTTGCCGGCCGATTACAGT 60.744 57.895 30.73 0.00 0.00 3.55
766 815 1.429148 GAGTTGCCGGCCGATTACAG 61.429 60.000 30.73 10.02 0.00 2.74
767 816 1.448893 GAGTTGCCGGCCGATTACA 60.449 57.895 30.73 16.45 0.00 2.41
768 817 2.522638 CGAGTTGCCGGCCGATTAC 61.523 63.158 30.73 20.19 0.00 1.89
769 818 2.023414 ATCGAGTTGCCGGCCGATTA 62.023 55.000 30.73 9.58 38.42 1.75
770 819 3.385749 ATCGAGTTGCCGGCCGATT 62.386 57.895 30.73 12.70 38.42 3.34
771 820 3.792053 GATCGAGTTGCCGGCCGAT 62.792 63.158 30.08 30.08 43.38 4.18
772 821 4.508128 GATCGAGTTGCCGGCCGA 62.508 66.667 30.73 25.30 35.43 5.54
773 822 2.622903 TAAGATCGAGTTGCCGGCCG 62.623 60.000 26.77 21.04 0.00 6.13
774 823 1.143183 TAAGATCGAGTTGCCGGCC 59.857 57.895 26.77 9.73 0.00 6.13
775 824 1.152383 GGTAAGATCGAGTTGCCGGC 61.152 60.000 22.73 22.73 0.00 6.13
776 825 0.529992 GGGTAAGATCGAGTTGCCGG 60.530 60.000 0.00 0.00 30.80 6.13
779 828 2.094182 TGTGAGGGTAAGATCGAGTTGC 60.094 50.000 0.00 0.00 0.00 4.17
861 915 4.500116 GGAGGCGGCTCGTGAGTC 62.500 72.222 29.95 13.32 0.00 3.36
873 927 2.354773 CGGATTAGCGACGGAGGC 60.355 66.667 0.00 0.00 0.00 4.70
874 928 2.354773 GCGGATTAGCGACGGAGG 60.355 66.667 0.00 0.00 0.00 4.30
928 996 2.540228 GGCGCCTTTATACCACCGC 61.540 63.158 22.15 0.00 40.58 5.68
1050 1118 3.535962 GAGGCGGGCAGAGAGAGG 61.536 72.222 3.78 0.00 0.00 3.69
1173 1241 4.514577 CCGGTGTAGGCAGCCTCG 62.515 72.222 20.38 15.55 39.77 4.63
1191 1262 0.806102 CGATGACCGGGCACTTGTAG 60.806 60.000 15.41 0.00 33.91 2.74
1313 1394 0.234884 GGCGCAGTTTGTGTACAGTC 59.765 55.000 10.83 0.00 0.00 3.51
1322 1403 0.806868 ATGAGTCATGGCGCAGTTTG 59.193 50.000 10.83 0.16 0.00 2.93
1341 1422 0.959867 CACGACCATGGCAATCACCA 60.960 55.000 13.04 0.00 45.82 4.17
1342 1423 1.802636 CACGACCATGGCAATCACC 59.197 57.895 13.04 0.00 0.00 4.02
1343 1424 1.137404 GCACGACCATGGCAATCAC 59.863 57.895 13.04 0.00 0.00 3.06
1344 1425 0.680601 ATGCACGACCATGGCAATCA 60.681 50.000 13.04 4.15 41.43 2.57
1345 1426 0.248743 CATGCACGACCATGGCAATC 60.249 55.000 13.04 0.44 41.43 2.67
1346 1427 0.680601 TCATGCACGACCATGGCAAT 60.681 50.000 13.04 0.00 42.19 3.56
1347 1428 1.303155 TCATGCACGACCATGGCAA 60.303 52.632 13.04 0.00 42.19 4.52
1348 1429 2.039974 GTCATGCACGACCATGGCA 61.040 57.895 13.04 3.48 44.92 4.92
1349 1430 1.378882 ATGTCATGCACGACCATGGC 61.379 55.000 13.04 14.58 45.58 4.40
1350 1431 0.379316 CATGTCATGCACGACCATGG 59.621 55.000 10.88 11.19 42.19 3.66
1351 1432 3.909957 CATGTCATGCACGACCATG 57.090 52.632 10.88 10.16 43.04 3.66
1409 1494 2.159476 TCAAACCTACGTACAGCGCTAG 60.159 50.000 10.99 7.53 46.11 3.42
1437 1522 2.163818 TCATCCGCGTCAAAAAGTCT 57.836 45.000 4.92 0.00 0.00 3.24
1485 1570 3.599285 CTGGTTACGGCCCAGCGAA 62.599 63.158 0.00 0.00 42.81 4.70
1604 1693 1.654501 CGTGTATGTGCATGAATCGCG 60.655 52.381 0.00 0.00 0.00 5.87
1610 1699 0.461870 GAGGGCGTGTATGTGCATGA 60.462 55.000 0.00 0.00 0.00 3.07
1618 1707 3.861131 GCAAGAATATCGAGGGCGTGTAT 60.861 47.826 0.00 0.00 38.98 2.29
1626 1715 2.797156 CCGAACAGCAAGAATATCGAGG 59.203 50.000 0.00 0.00 32.38 4.63
1639 1742 1.215382 GCCCAAATTCCCGAACAGC 59.785 57.895 0.00 0.00 0.00 4.40
1640 1743 0.958382 TCGCCCAAATTCCCGAACAG 60.958 55.000 0.00 0.00 0.00 3.16
1645 1748 3.119280 AGTTAATTTCGCCCAAATTCCCG 60.119 43.478 4.65 0.00 42.68 5.14
1648 1752 7.088272 AGTTGTAGTTAATTTCGCCCAAATTC 58.912 34.615 4.65 0.00 42.68 2.17
1661 1765 9.649167 GTACATGTCCAAGTAGTTGTAGTTAAT 57.351 33.333 0.00 0.00 30.95 1.40
1665 1769 5.336213 CGGTACATGTCCAAGTAGTTGTAGT 60.336 44.000 0.00 3.36 30.95 2.73
1666 1770 5.100259 CGGTACATGTCCAAGTAGTTGTAG 58.900 45.833 0.00 0.00 30.95 2.74
1667 1771 4.082081 CCGGTACATGTCCAAGTAGTTGTA 60.082 45.833 0.00 0.00 30.95 2.41
1671 1775 1.829222 CCCGGTACATGTCCAAGTAGT 59.171 52.381 0.00 0.00 0.00 2.73
1673 1777 0.538118 GCCCGGTACATGTCCAAGTA 59.462 55.000 0.00 0.00 0.00 2.24
1674 1778 1.298667 GCCCGGTACATGTCCAAGT 59.701 57.895 0.00 0.00 0.00 3.16
1676 1780 2.672295 GGCCCGGTACATGTCCAA 59.328 61.111 0.00 0.00 0.00 3.53
1691 1809 3.827898 AGCTCGTACTCCTGCGGC 61.828 66.667 0.00 0.00 0.00 6.53
1693 1811 2.103143 CCAGCTCGTACTCCTGCG 59.897 66.667 0.00 0.00 0.00 5.18
1871 1989 2.755469 GGGCGTACGTACCCCTGA 60.755 66.667 30.15 0.00 40.56 3.86
1901 2019 3.320673 AACGAAGCTAAACTGGAGAGG 57.679 47.619 0.00 0.00 0.00 3.69
1927 2045 3.735746 GTGTCAATTTTAGCTTGTGCACC 59.264 43.478 15.69 0.00 42.74 5.01
1959 2077 0.036483 ACACAGCACACACAGTCACA 60.036 50.000 0.00 0.00 0.00 3.58
1960 2078 0.374758 CACACAGCACACACAGTCAC 59.625 55.000 0.00 0.00 0.00 3.67
1961 2079 1.368345 GCACACAGCACACACAGTCA 61.368 55.000 0.00 0.00 44.79 3.41
1962 2080 1.353103 GCACACAGCACACACAGTC 59.647 57.895 0.00 0.00 44.79 3.51
1963 2081 3.501396 GCACACAGCACACACAGT 58.499 55.556 0.00 0.00 44.79 3.55
1972 2090 0.322456 TAATCCCACCTGCACACAGC 60.322 55.000 0.00 0.00 43.02 4.40
1973 2091 1.271325 TGTAATCCCACCTGCACACAG 60.271 52.381 0.00 0.00 44.05 3.66
1974 2092 0.767998 TGTAATCCCACCTGCACACA 59.232 50.000 0.00 0.00 0.00 3.72
1975 2093 1.745087 CATGTAATCCCACCTGCACAC 59.255 52.381 0.00 0.00 0.00 3.82
2029 2147 2.671070 CTGGAACGCCACCATCCT 59.329 61.111 0.00 0.00 39.92 3.24
2176 2294 3.753272 GTGTGAGCCATGTGTGATTACTT 59.247 43.478 0.00 0.00 0.00 2.24
2322 2442 1.613630 AGCCAATGGGACCGTCTCT 60.614 57.895 0.00 0.00 35.59 3.10
2338 2458 2.743928 CGTGGAGTTGAGCCCAGC 60.744 66.667 0.00 0.00 32.28 4.85
2642 2767 9.301153 GGAAAATAATTAATACCAACACTGCAG 57.699 33.333 13.48 13.48 0.00 4.41
2676 2801 0.674581 ACATGACACATCCACAGCGG 60.675 55.000 0.00 0.00 0.00 5.52
2691 2817 3.568430 TGTCTACCTATACCGCTCACATG 59.432 47.826 0.00 0.00 0.00 3.21
2708 2834 7.601705 TGTACATCCTCATCAATCATGTCTA 57.398 36.000 0.00 0.00 33.66 2.59
2723 2849 7.830697 TGTCATTCAAAGATCAATGTACATCCT 59.169 33.333 9.23 1.81 32.67 3.24
2747 2873 0.179468 ACGTGTGGGCTACTGTTTGT 59.821 50.000 1.79 0.00 0.00 2.83
2754 2880 3.332034 ACTAATCAAACGTGTGGGCTAC 58.668 45.455 5.75 0.00 0.00 3.58
2755 2881 3.688694 ACTAATCAAACGTGTGGGCTA 57.311 42.857 5.75 0.00 0.00 3.93
2759 2885 6.656314 TGCTATTACTAATCAAACGTGTGG 57.344 37.500 5.75 0.00 0.00 4.17
2811 2937 9.770097 TCATGAATTTTAAGCACATGGTAAAAA 57.230 25.926 0.00 0.00 38.82 1.94
2812 2938 9.421806 CTCATGAATTTTAAGCACATGGTAAAA 57.578 29.630 0.00 3.35 38.82 1.52
2813 2939 8.801299 TCTCATGAATTTTAAGCACATGGTAAA 58.199 29.630 0.00 0.00 38.82 2.01
2814 2940 8.347004 TCTCATGAATTTTAAGCACATGGTAA 57.653 30.769 0.00 0.00 38.82 2.85
2816 2942 6.839124 TCTCATGAATTTTAAGCACATGGT 57.161 33.333 0.00 0.00 38.82 3.55
2839 2966 4.808364 AGCGTTTTGTTTGCACATACAATT 59.192 33.333 7.35 0.00 33.51 2.32
2847 2974 1.851658 ATGGAGCGTTTTGTTTGCAC 58.148 45.000 0.00 0.00 0.00 4.57
3013 3142 6.327934 AGATTGAGGAAATTTTTGAGATGCG 58.672 36.000 0.00 0.00 0.00 4.73
3021 3150 9.551734 CTTTGGAGAAAGATTGAGGAAATTTTT 57.448 29.630 0.00 0.00 41.12 1.94
3044 3173 5.602561 AGAAACTACTTGGGGCAATTTCTTT 59.397 36.000 0.00 0.00 30.02 2.52
3058 3187 5.071923 AGGGAGTGCAAGTTAGAAACTACTT 59.928 40.000 0.00 0.00 41.91 2.24
3062 3191 3.244596 GGAGGGAGTGCAAGTTAGAAACT 60.245 47.826 0.00 0.00 45.46 2.66
3079 3208 6.966534 TTATACTAACTTTAGGACGGAGGG 57.033 41.667 1.21 0.00 35.08 4.30
3122 3251 8.611051 AAATTAGTTATGTAGTCCCTCTGTCT 57.389 34.615 0.00 0.00 0.00 3.41
3145 3274 4.590647 TGATGGACCCTTATTTGTGCAAAA 59.409 37.500 1.26 0.00 36.39 2.44
3175 3305 5.810080 ACAAAATATTTCCCCCGTCAAAA 57.190 34.783 0.10 0.00 0.00 2.44
3181 3311 4.097286 CCTGTGTACAAAATATTTCCCCCG 59.903 45.833 0.00 0.00 0.00 5.73
3197 3327 8.383175 AGTTCTTTGGATAGATTTTCCTGTGTA 58.617 33.333 0.00 0.00 34.17 2.90
3201 3331 6.376581 AGCAGTTCTTTGGATAGATTTTCCTG 59.623 38.462 0.00 0.00 34.17 3.86
3246 3376 6.858993 GGCGATCTTTAGTTCTACTAGTGATG 59.141 42.308 5.39 0.00 31.47 3.07
3257 3387 4.095036 CCCTGAAAAGGCGATCTTTAGTTC 59.905 45.833 4.94 1.48 44.30 3.01
3259 3389 3.610911 CCCTGAAAAGGCGATCTTTAGT 58.389 45.455 4.94 0.00 44.30 2.24
3269 3399 0.540597 AGTGCTTCCCCTGAAAAGGC 60.541 55.000 0.00 0.00 0.00 4.35
3276 3406 8.697507 ATATCTTTAATTTAGTGCTTCCCCTG 57.302 34.615 0.00 0.00 0.00 4.45
3300 3430 7.308348 CCAAAGTGGTTGATTCGTTGTTAGTAT 60.308 37.037 0.00 0.00 39.87 2.12
3307 3437 2.223688 TGCCAAAGTGGTTGATTCGTTG 60.224 45.455 0.00 0.00 40.46 4.10
3324 3454 1.113788 AAACTCAAGCTTGCTTGCCA 58.886 45.000 25.33 12.11 34.56 4.92
3337 3467 2.417339 CGACTCCTTCGTCAAACTCA 57.583 50.000 0.00 0.00 43.24 3.41
3383 3513 8.097078 TGCTGTTTCCCAAAATAATGAAAATG 57.903 30.769 0.00 0.00 0.00 2.32
3549 3684 8.748412 CCATGTATTTTAAGAATGTTCTTCCCA 58.252 33.333 11.02 2.49 43.72 4.37


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

AutoCloner maintained by Alex Coulton.