Multiple sequence alignment - TraesCS1D01G391300

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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 TraesCS1D01G391300 chr1D 100.000 2998 0 0 1 2998 462147482 462150479 0.000000e+00 5537.0
1 TraesCS1D01G391300 chr1A 89.823 2260 102 50 1 2202 554017246 554019435 0.000000e+00 2782.0
2 TraesCS1D01G391300 chr1A 93.750 80 5 0 2249 2328 554019562 554019641 1.460000e-23 121.0
3 TraesCS1D01G391300 chr1A 91.304 46 2 2 1901 1945 508628933 508628977 8.970000e-06 62.1
4 TraesCS1D01G391300 chr1B 93.026 1907 69 20 1 1859 636794982 636796872 0.000000e+00 2726.0
5 TraesCS1D01G391300 chr1B 92.857 168 7 4 1997 2162 636796997 636797161 3.860000e-59 239.0
6 TraesCS1D01G391300 chr1B 88.889 81 8 1 1867 1946 636796917 636796997 6.840000e-17 99.0
7 TraesCS1D01G391300 chr3B 87.171 951 90 22 798 1731 23360665 23361600 0.000000e+00 1051.0
8 TraesCS1D01G391300 chr3B 89.804 255 15 4 2001 2244 8547718 8547972 1.730000e-82 316.0
9 TraesCS1D01G391300 chr3B 84.375 96 14 1 2349 2443 823147479 823147384 3.180000e-15 93.5
10 TraesCS1D01G391300 chr3B 73.540 291 43 21 2708 2977 228393931 228393654 2.480000e-11 80.5
11 TraesCS1D01G391300 chr3B 88.462 52 4 2 1903 1954 398840444 398840395 8.970000e-06 62.1
12 TraesCS1D01G391300 chr3B 90.909 44 4 0 1903 1946 685396025 685395982 3.230000e-05 60.2
13 TraesCS1D01G391300 chr5A 86.472 961 93 25 798 1741 632263654 632262714 0.000000e+00 1020.0
14 TraesCS1D01G391300 chr6B 81.744 493 67 16 2359 2839 719329448 719328967 1.010000e-104 390.0
15 TraesCS1D01G391300 chr6B 100.000 30 0 0 1902 1931 197455902 197455931 4.170000e-04 56.5
16 TraesCS1D01G391300 chr2D 82.436 427 56 16 2348 2767 480178002 480177588 3.680000e-94 355.0
17 TraesCS1D01G391300 chr2D 81.385 231 24 1 1972 2202 15335337 15335548 1.430000e-38 171.0
18 TraesCS1D01G391300 chr6A 87.234 235 22 5 909 1139 2845440 2845670 8.240000e-66 261.0
19 TraesCS1D01G391300 chr7A 76.021 563 95 34 2348 2899 550247 549714 3.840000e-64 255.0
20 TraesCS1D01G391300 chr2B 79.026 267 41 12 2604 2858 239621755 239621492 5.140000e-38 169.0
21 TraesCS1D01G391300 chr4D 97.561 41 1 0 1906 1946 107440577 107440537 1.490000e-08 71.3
22 TraesCS1D01G391300 chr4B 95.122 41 2 0 1906 1946 169582375 169582415 6.940000e-07 65.8
23 TraesCS1D01G391300 chr6D 89.796 49 5 0 1899 1947 43056136 43056088 2.490000e-06 63.9
24 TraesCS1D01G391300 chr3D 88.462 52 4 2 1903 1954 320835083 320835034 8.970000e-06 62.1


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 TraesCS1D01G391300 chr1D 462147482 462150479 2997 False 5537.000000 5537 100.000000 1 2998 1 chr1D.!!$F1 2997
1 TraesCS1D01G391300 chr1A 554017246 554019641 2395 False 1451.500000 2782 91.786500 1 2328 2 chr1A.!!$F2 2327
2 TraesCS1D01G391300 chr1B 636794982 636797161 2179 False 1021.333333 2726 91.590667 1 2162 3 chr1B.!!$F1 2161
3 TraesCS1D01G391300 chr3B 23360665 23361600 935 False 1051.000000 1051 87.171000 798 1731 1 chr3B.!!$F2 933
4 TraesCS1D01G391300 chr5A 632262714 632263654 940 True 1020.000000 1020 86.472000 798 1741 1 chr5A.!!$R1 943
5 TraesCS1D01G391300 chr7A 549714 550247 533 True 255.000000 255 76.021000 2348 2899 1 chr7A.!!$R1 551

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
847 875 0.179034 GCTGTCCATCCATCCTCACC 60.179 60.0 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2114 2248 0.251209 GTCTCCAACCTTTCACCCCC 60.251 60.0 0.0 0.0 0.0 5.4 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
106 108 6.183361 TGCATCTATACATGGCAAACTCTACT 60.183 38.462 0.00 0.00 0.00 2.57
275 277 3.247442 GAATGCATTGTGTGTGACATGG 58.753 45.455 18.59 0.00 33.40 3.66
299 304 0.322648 TGGGATGTGCTCAGTCTGTG 59.677 55.000 0.00 0.00 0.00 3.66
411 416 5.705441 AGATGCAGTCAAACGAAGGAAATAA 59.295 36.000 0.00 0.00 0.00 1.40
412 417 5.356882 TGCAGTCAAACGAAGGAAATAAG 57.643 39.130 0.00 0.00 0.00 1.73
581 587 8.484575 ACAGTACTCAGTAGCTAGATACTACAA 58.515 37.037 19.77 8.30 42.04 2.41
607 613 5.972935 ACACGATGGAAATATATGCCGATA 58.027 37.500 0.00 0.00 0.00 2.92
633 639 3.099267 AGTTTGTGTCTCCTCAACTCG 57.901 47.619 0.00 0.00 0.00 4.18
685 696 1.001641 CCTGAGGGAAAGTGGGCTG 60.002 63.158 0.00 0.00 33.58 4.85
746 757 1.377536 GAGAGCATTGTTCTGAGGGC 58.622 55.000 7.83 0.00 0.00 5.19
847 875 0.179034 GCTGTCCATCCATCCTCACC 60.179 60.000 0.00 0.00 0.00 4.02
1023 1078 0.374758 GCATCACACATACACCGCAG 59.625 55.000 0.00 0.00 0.00 5.18
1030 1085 0.601576 ACATACACCGCAGCAAACGA 60.602 50.000 0.00 0.00 0.00 3.85
1425 1481 2.642996 CTATGGCGGCACATCCACGA 62.643 60.000 16.34 0.00 33.60 4.35
1433 1489 3.387947 ACATCCACGACGACCCCC 61.388 66.667 0.00 0.00 0.00 5.40
1505 1561 1.534697 GTTGGTGGTGGACCTGGAA 59.465 57.895 0.00 0.00 46.32 3.53
1562 1618 2.117779 GCTTAGGCTTGGCTGCTCC 61.118 63.158 6.97 0.00 35.22 4.70
1567 1623 2.350514 GCTTGGCTGCTCCTGAGT 59.649 61.111 0.00 0.00 35.26 3.41
1609 1668 7.931046 TGACATTATAATCCATCCATCCATCA 58.069 34.615 0.00 0.00 0.00 3.07
1613 1672 9.642343 CATTATAATCCATCCATCCATCAATCT 57.358 33.333 0.00 0.00 0.00 2.40
1815 1890 4.394300 TGGTTGGTTTGCAATGAAAACTTG 59.606 37.500 15.72 0.00 37.60 3.16
1850 1925 4.397382 CTTGTTCAACTATGCATGTGTCG 58.603 43.478 10.16 0.00 0.00 4.35
1859 1934 5.050490 ACTATGCATGTGTCGGATTTACTC 58.950 41.667 10.16 0.00 0.00 2.59
1860 1935 2.627945 TGCATGTGTCGGATTTACTCC 58.372 47.619 0.00 0.00 41.07 3.85
1863 1938 3.458189 CATGTGTCGGATTTACTCCCTC 58.542 50.000 0.00 0.00 41.49 4.30
1871 1983 2.966516 GGATTTACTCCCTCCGATCAGT 59.033 50.000 0.00 0.00 38.19 3.41
1922 2035 0.415830 TGTACTCCCTCCATCCCACA 59.584 55.000 0.00 0.00 0.00 4.17
1932 2045 4.350816 CCCTCCATCCCACAATATAAGACA 59.649 45.833 0.00 0.00 0.00 3.41
1935 2048 7.006509 CCTCCATCCCACAATATAAGACATTT 58.993 38.462 0.00 0.00 0.00 2.32
1936 2049 7.175641 CCTCCATCCCACAATATAAGACATTTC 59.824 40.741 0.00 0.00 0.00 2.17
1938 2051 8.944138 TCCATCCCACAATATAAGACATTTCTA 58.056 33.333 0.00 0.00 0.00 2.10
1952 2065 8.635877 AAGACATTTCTACAAGCTATAAGACG 57.364 34.615 0.00 0.00 0.00 4.18
1953 2066 7.773149 AGACATTTCTACAAGCTATAAGACGT 58.227 34.615 0.00 0.00 0.00 4.34
1956 2069 9.216117 ACATTTCTACAAGCTATAAGACGTTTT 57.784 29.630 0.00 0.00 0.00 2.43
1959 2072 7.057149 TCTACAAGCTATAAGACGTTTTTGC 57.943 36.000 0.00 0.21 0.00 3.68
1963 2076 3.060363 AGCTATAAGACGTTTTTGCGACG 59.940 43.478 0.00 0.00 45.46 5.12
1964 2077 2.867456 ATAAGACGTTTTTGCGACGG 57.133 45.000 0.00 0.00 44.34 4.79
1969 2082 1.957186 CGTTTTTGCGACGGAGGGA 60.957 57.895 0.00 0.00 36.90 4.20
1970 2083 1.500512 CGTTTTTGCGACGGAGGGAA 61.501 55.000 0.00 0.00 36.90 3.97
2113 2247 4.978083 AGTCCGCTCGAAACTAATTAGA 57.022 40.909 19.38 0.00 0.00 2.10
2114 2248 4.922719 AGTCCGCTCGAAACTAATTAGAG 58.077 43.478 19.38 6.87 41.97 2.43
2115 2249 4.043073 GTCCGCTCGAAACTAATTAGAGG 58.957 47.826 19.38 2.60 40.12 3.69
2116 2250 3.067742 TCCGCTCGAAACTAATTAGAGGG 59.932 47.826 19.38 12.75 46.40 4.30
2117 2251 3.381949 CGCTCGAAACTAATTAGAGGGG 58.618 50.000 19.38 6.02 44.53 4.79
2118 2252 3.729966 GCTCGAAACTAATTAGAGGGGG 58.270 50.000 19.38 6.34 40.12 5.40
2119 2253 3.134262 GCTCGAAACTAATTAGAGGGGGT 59.866 47.826 19.38 0.00 40.12 4.95
2120 2254 4.694339 CTCGAAACTAATTAGAGGGGGTG 58.306 47.826 19.38 2.69 37.19 4.61
2121 2255 4.355549 TCGAAACTAATTAGAGGGGGTGA 58.644 43.478 19.38 4.81 0.00 4.02
2122 2256 4.778958 TCGAAACTAATTAGAGGGGGTGAA 59.221 41.667 19.38 0.00 0.00 3.18
2123 2257 5.248934 TCGAAACTAATTAGAGGGGGTGAAA 59.751 40.000 19.38 0.00 0.00 2.69
2124 2258 5.585047 CGAAACTAATTAGAGGGGGTGAAAG 59.415 44.000 19.38 0.00 0.00 2.62
2125 2259 5.452341 AACTAATTAGAGGGGGTGAAAGG 57.548 43.478 19.38 0.00 0.00 3.11
2126 2260 4.445564 ACTAATTAGAGGGGGTGAAAGGT 58.554 43.478 19.38 0.00 0.00 3.50
2127 2261 4.856182 ACTAATTAGAGGGGGTGAAAGGTT 59.144 41.667 19.38 0.00 0.00 3.50
2128 2262 3.739401 ATTAGAGGGGGTGAAAGGTTG 57.261 47.619 0.00 0.00 0.00 3.77
2129 2263 1.368374 TAGAGGGGGTGAAAGGTTGG 58.632 55.000 0.00 0.00 0.00 3.77
2179 2313 5.753438 CCAAATCGCTCTACTAAGCAACATA 59.247 40.000 0.00 0.00 42.62 2.29
2195 2329 5.764686 AGCAACATACAGTGAAAATGAGACA 59.235 36.000 0.00 0.00 34.17 3.41
2208 2384 7.604164 GTGAAAATGAGACAAATACTGAGAGGA 59.396 37.037 0.00 0.00 0.00 3.71
2212 2388 7.673641 ATGAGACAAATACTGAGAGGAAGAT 57.326 36.000 0.00 0.00 0.00 2.40
2230 2406 3.112709 GTGAGCGCGTGAGGTTCC 61.113 66.667 8.43 0.00 0.00 3.62
2265 2479 7.778853 TCAGGTACCTAATCCTTTGACTAGTAG 59.221 40.741 15.80 0.00 30.91 2.57
2268 2482 9.413734 GGTACCTAATCCTTTGACTAGTAGTAA 57.586 37.037 4.06 0.00 0.00 2.24
2283 2497 9.886132 GACTAGTAGTAATCTTTGATTTTGGGA 57.114 33.333 1.88 0.00 0.00 4.37
2290 2504 4.042271 TCTTTGATTTTGGGACCCCTAC 57.958 45.455 8.45 0.00 36.94 3.18
2328 2542 0.621571 AACTGGGGAGCTCCTATGCA 60.622 55.000 31.36 5.84 35.95 3.96
2329 2543 0.621571 ACTGGGGAGCTCCTATGCAA 60.622 55.000 31.36 8.18 35.95 4.08
2330 2544 0.179034 CTGGGGAGCTCCTATGCAAC 60.179 60.000 31.36 13.25 35.95 4.17
2331 2545 1.227674 GGGGAGCTCCTATGCAACG 60.228 63.158 31.36 0.00 35.95 4.10
2332 2546 1.889573 GGGAGCTCCTATGCAACGC 60.890 63.158 31.36 8.41 35.95 4.84
2333 2547 1.144936 GGAGCTCCTATGCAACGCT 59.855 57.895 26.25 0.00 34.99 5.07
2334 2548 1.156645 GGAGCTCCTATGCAACGCTG 61.157 60.000 26.25 0.00 34.99 5.18
2335 2549 0.460987 GAGCTCCTATGCAACGCTGT 60.461 55.000 0.87 0.00 34.99 4.40
2336 2550 0.824109 AGCTCCTATGCAACGCTGTA 59.176 50.000 0.00 0.00 34.99 2.74
2337 2551 1.202463 AGCTCCTATGCAACGCTGTAG 60.202 52.381 0.00 0.00 34.99 2.74
2338 2552 1.858091 CTCCTATGCAACGCTGTAGG 58.142 55.000 2.85 2.85 38.22 3.18
2339 2553 0.179084 TCCTATGCAACGCTGTAGGC 60.179 55.000 4.23 0.00 37.45 3.93
2340 2554 0.461870 CCTATGCAACGCTGTAGGCA 60.462 55.000 0.00 9.19 41.91 4.75
2341 2555 0.933097 CTATGCAACGCTGTAGGCAG 59.067 55.000 0.00 0.00 45.23 4.85
2342 2556 0.249120 TATGCAACGCTGTAGGCAGT 59.751 50.000 0.00 0.00 44.32 4.40
2343 2557 1.021390 ATGCAACGCTGTAGGCAGTC 61.021 55.000 0.00 0.00 44.32 3.51
2344 2558 1.667830 GCAACGCTGTAGGCAGTCA 60.668 57.895 0.00 0.00 44.32 3.41
2345 2559 1.227999 GCAACGCTGTAGGCAGTCAA 61.228 55.000 0.00 0.00 44.32 3.18
2346 2560 0.512952 CAACGCTGTAGGCAGTCAAC 59.487 55.000 0.00 0.00 44.32 3.18
2407 2621 1.297893 GCTTCATTGATCGCCACGC 60.298 57.895 0.00 0.00 0.00 5.34
2437 2651 1.222115 GCTCGAGCGTTGTTTCACCT 61.222 55.000 23.61 0.00 0.00 4.00
2440 2654 1.067364 TCGAGCGTTGTTTCACCTGTA 59.933 47.619 0.00 0.00 0.00 2.74
2441 2655 1.455786 CGAGCGTTGTTTCACCTGTAG 59.544 52.381 0.00 0.00 0.00 2.74
2443 2657 1.202651 AGCGTTGTTTCACCTGTAGCT 60.203 47.619 0.00 0.00 0.00 3.32
2444 2658 1.194772 GCGTTGTTTCACCTGTAGCTC 59.805 52.381 0.00 0.00 0.00 4.09
2445 2659 2.479837 CGTTGTTTCACCTGTAGCTCA 58.520 47.619 0.00 0.00 0.00 4.26
2446 2660 2.869801 CGTTGTTTCACCTGTAGCTCAA 59.130 45.455 0.00 0.00 0.00 3.02
2478 2692 2.289547 CGTTGTTTCACCTCCGTTGAAT 59.710 45.455 0.00 0.00 0.00 2.57
2516 2741 9.535878 AAAAACTGTAAAAATTCGCTAAATGGA 57.464 25.926 0.00 0.00 0.00 3.41
2517 2742 9.535878 AAAACTGTAAAAATTCGCTAAATGGAA 57.464 25.926 0.00 0.00 0.00 3.53
2518 2743 9.535878 AAACTGTAAAAATTCGCTAAATGGAAA 57.464 25.926 0.00 0.00 0.00 3.13
2519 2744 9.705290 AACTGTAAAAATTCGCTAAATGGAAAT 57.295 25.926 0.00 0.00 0.00 2.17
2520 2745 9.705290 ACTGTAAAAATTCGCTAAATGGAAATT 57.295 25.926 0.00 0.00 0.00 1.82
2603 2828 5.940617 TCAAATTTGGAAGAGAACTCCTCA 58.059 37.500 17.90 0.00 44.40 3.86
2608 2833 7.846101 ATTTGGAAGAGAACTCCTCAAATTT 57.154 32.000 15.00 0.00 44.40 1.82
2613 2838 7.142021 GGAAGAGAACTCCTCAAATTTGAAAC 58.858 38.462 20.82 9.25 44.40 2.78
2615 2840 7.830099 AGAGAACTCCTCAAATTTGAAACAT 57.170 32.000 20.82 7.45 44.40 2.71
2616 2841 8.924511 AGAGAACTCCTCAAATTTGAAACATA 57.075 30.769 20.82 5.19 44.40 2.29
2620 2845 9.912634 GAACTCCTCAAATTTGAAACATATTCA 57.087 29.630 20.82 0.00 36.64 2.57
2724 2949 9.449550 TTCATCGATATTGGAAAATTTTCATCG 57.550 29.630 28.23 28.23 39.07 3.84
2725 2950 8.075574 TCATCGATATTGGAAAATTTTCATCGG 58.924 33.333 30.61 22.57 38.65 4.18
2726 2951 7.561021 TCGATATTGGAAAATTTTCATCGGA 57.439 32.000 30.61 21.80 38.65 4.55
2727 2952 8.165239 TCGATATTGGAAAATTTTCATCGGAT 57.835 30.769 30.61 19.45 38.65 4.18
2728 2953 8.629158 TCGATATTGGAAAATTTTCATCGGATT 58.371 29.630 30.61 14.83 38.65 3.01
2729 2954 9.248291 CGATATTGGAAAATTTTCATCGGATTT 57.752 29.630 27.33 13.74 36.53 2.17
2813 3038 7.565323 TTTGAAAAAGGTTCATTGGATTTGG 57.435 32.000 0.00 0.00 0.00 3.28
2816 3041 7.341805 TGAAAAAGGTTCATTGGATTTGGAAA 58.658 30.769 0.00 0.00 0.00 3.13
2817 3042 7.831193 TGAAAAAGGTTCATTGGATTTGGAAAA 59.169 29.630 0.00 0.00 0.00 2.29
2818 3043 8.586879 AAAAAGGTTCATTGGATTTGGAAAAA 57.413 26.923 0.00 0.00 0.00 1.94
2841 3066 9.911138 AAAAAGTTCATGCATTTTGAAAAAGTT 57.089 22.222 0.00 0.00 35.03 2.66
2842 3067 9.558648 AAAAGTTCATGCATTTTGAAAAAGTTC 57.441 25.926 0.00 0.00 35.03 3.01
2843 3068 7.846644 AGTTCATGCATTTTGAAAAAGTTCA 57.153 28.000 0.00 0.00 42.12 3.18
2844 3069 8.441312 AGTTCATGCATTTTGAAAAAGTTCAT 57.559 26.923 0.00 0.00 43.29 2.57
2845 3070 8.553696 AGTTCATGCATTTTGAAAAAGTTCATC 58.446 29.630 0.00 0.00 43.29 2.92
2846 3071 7.107834 TCATGCATTTTGAAAAAGTTCATCG 57.892 32.000 0.00 0.00 43.29 3.84
2847 3072 5.903764 TGCATTTTGAAAAAGTTCATCGG 57.096 34.783 0.00 0.00 43.29 4.18
2848 3073 5.595885 TGCATTTTGAAAAAGTTCATCGGA 58.404 33.333 0.00 0.00 43.29 4.55
2849 3074 6.222389 TGCATTTTGAAAAAGTTCATCGGAT 58.778 32.000 0.00 0.00 43.29 4.18
2850 3075 6.705381 TGCATTTTGAAAAAGTTCATCGGATT 59.295 30.769 0.00 0.00 43.29 3.01
2851 3076 7.226325 TGCATTTTGAAAAAGTTCATCGGATTT 59.774 29.630 0.00 0.00 43.29 2.17
2852 3077 7.531534 GCATTTTGAAAAAGTTCATCGGATTTG 59.468 33.333 0.00 0.00 43.29 2.32
2853 3078 8.763356 CATTTTGAAAAAGTTCATCGGATTTGA 58.237 29.630 0.00 0.00 43.29 2.69
2854 3079 8.709386 TTTTGAAAAAGTTCATCGGATTTGAA 57.291 26.923 0.00 0.00 43.29 2.69
2855 3080 8.709386 TTTGAAAAAGTTCATCGGATTTGAAA 57.291 26.923 0.00 0.00 43.29 2.69
2856 3081 8.709386 TTGAAAAAGTTCATCGGATTTGAAAA 57.291 26.923 0.00 0.00 43.29 2.29
2857 3082 8.709386 TGAAAAAGTTCATCGGATTTGAAAAA 57.291 26.923 0.00 0.00 38.88 1.94
2897 3122 6.648879 AAAAAGTCCATCGGATTTGAGAAA 57.351 33.333 0.00 0.00 32.02 2.52
2898 3123 6.648879 AAAAGTCCATCGGATTTGAGAAAA 57.351 33.333 0.00 0.00 32.02 2.29
2899 3124 6.648879 AAAGTCCATCGGATTTGAGAAAAA 57.351 33.333 0.00 0.00 32.02 1.94
2900 3125 5.886960 AGTCCATCGGATTTGAGAAAAAG 57.113 39.130 0.00 0.00 32.73 2.27
2901 3126 5.316987 AGTCCATCGGATTTGAGAAAAAGT 58.683 37.500 0.00 0.00 32.73 2.66
2904 3129 5.088739 CCATCGGATTTGAGAAAAAGTTCG 58.911 41.667 0.00 0.00 38.90 3.95
2962 3226 9.767684 AAAGTTCGTTGATTTTGGAAAAATTTC 57.232 25.926 0.00 0.00 36.46 2.17
2964 3228 9.108284 AGTTCGTTGATTTTGGAAAAATTTCAT 57.892 25.926 8.06 0.00 38.92 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
106 108 4.955450 CCATGATGGTAACCCAAAGATGAA 59.045 41.667 2.54 0.00 46.04 2.57
275 277 0.176680 ACTGAGCACATCCCATCGAC 59.823 55.000 0.00 0.00 0.00 4.20
401 406 3.368427 GCCTTTGCCACCTTATTTCCTTC 60.368 47.826 0.00 0.00 0.00 3.46
525 531 4.081087 TGCTTCTAACTTACTCCATGGGAC 60.081 45.833 13.02 0.00 0.00 4.46
527 533 4.487714 TGCTTCTAACTTACTCCATGGG 57.512 45.455 13.02 5.22 0.00 4.00
581 587 4.631377 CGGCATATATTTCCATCGTGTCAT 59.369 41.667 0.00 0.00 0.00 3.06
607 613 7.246171 AGTTGAGGAGACACAAACTACATAT 57.754 36.000 0.00 0.00 42.60 1.78
633 639 1.303282 CACCCAAAGAGGCCCCTAC 59.697 63.158 0.00 0.00 35.39 3.18
685 696 1.000060 ACATGTGTTGGCAATGTGCTC 60.000 47.619 1.92 0.00 44.28 4.26
746 757 1.153309 TGATGTGGCAGGCGAGATG 60.153 57.895 0.00 0.00 0.00 2.90
905 937 2.265589 TTTTCTCCTCGGACCCAAAC 57.734 50.000 0.00 0.00 0.00 2.93
1047 1103 0.106819 CCCCTGCTCTCCATCAAAGG 60.107 60.000 0.00 0.00 0.00 3.11
1250 1306 2.282180 ACGTTCATGTGCCCACCC 60.282 61.111 0.00 0.00 0.00 4.61
1334 1390 3.243816 TGGACAGCAGCAGGAGCA 61.244 61.111 0.00 0.00 45.49 4.26
1505 1561 4.400251 CCTCCTCCGACCCCCAGT 62.400 72.222 0.00 0.00 0.00 4.00
1567 1623 4.687901 TGTCAATCCTGAAGAGTCAACA 57.312 40.909 0.00 0.00 31.88 3.33
1583 1639 8.392479 TGATGGATGGATGGATTATAATGTCAA 58.608 33.333 1.78 0.00 0.00 3.18
1632 1691 2.002586 GTAGTCGTGCATGCAGACATT 58.997 47.619 32.68 23.04 37.36 2.71
1678 1739 0.681733 TTCTCGTTCTCTTGCCAGCT 59.318 50.000 0.00 0.00 0.00 4.24
1683 1744 0.859232 TGCGTTTCTCGTTCTCTTGC 59.141 50.000 0.00 0.00 42.13 4.01
1685 1746 2.128035 CACTGCGTTTCTCGTTCTCTT 58.872 47.619 0.00 0.00 42.13 2.85
1815 1890 1.888512 TGAACAAGCTCCAAAGGATGC 59.111 47.619 0.00 0.00 0.00 3.91
1859 1934 6.208797 TGTTACATATAGAACTGATCGGAGGG 59.791 42.308 9.00 0.00 0.00 4.30
1860 1935 7.215719 TGTTACATATAGAACTGATCGGAGG 57.784 40.000 9.00 0.00 0.00 4.30
1863 1938 8.642908 TGTTTGTTACATATAGAACTGATCGG 57.357 34.615 0.00 0.00 0.00 4.18
1935 2048 6.183360 CGCAAAAACGTCTTATAGCTTGTAGA 60.183 38.462 0.00 0.00 0.00 2.59
1936 2049 5.952064 CGCAAAAACGTCTTATAGCTTGTAG 59.048 40.000 0.00 0.00 0.00 2.74
1938 2051 4.449743 TCGCAAAAACGTCTTATAGCTTGT 59.550 37.500 0.00 0.00 0.00 3.16
1946 2059 1.788308 CTCCGTCGCAAAAACGTCTTA 59.212 47.619 0.00 0.00 38.44 2.10
1947 2060 0.580104 CTCCGTCGCAAAAACGTCTT 59.420 50.000 0.00 0.00 38.44 3.01
1949 2062 1.203313 CCTCCGTCGCAAAAACGTC 59.797 57.895 0.00 0.00 38.44 4.34
1950 2063 2.248835 CCCTCCGTCGCAAAAACGT 61.249 57.895 0.00 0.00 38.44 3.99
1951 2064 1.500512 TTCCCTCCGTCGCAAAAACG 61.501 55.000 0.00 0.00 39.78 3.60
1952 2065 0.879090 ATTCCCTCCGTCGCAAAAAC 59.121 50.000 0.00 0.00 0.00 2.43
1953 2066 2.476126 TATTCCCTCCGTCGCAAAAA 57.524 45.000 0.00 0.00 0.00 1.94
1956 2069 3.133362 AGTTAATATTCCCTCCGTCGCAA 59.867 43.478 0.00 0.00 0.00 4.85
1959 2072 5.503520 GCAAAAGTTAATATTCCCTCCGTCG 60.504 44.000 0.00 0.00 0.00 5.12
1963 2076 5.830000 ACGCAAAAGTTAATATTCCCTCC 57.170 39.130 0.00 0.00 0.00 4.30
1964 2077 7.982224 AGTAACGCAAAAGTTAATATTCCCTC 58.018 34.615 0.00 0.00 38.19 4.30
2113 2247 0.402861 TCTCCAACCTTTCACCCCCT 60.403 55.000 0.00 0.00 0.00 4.79
2114 2248 0.251209 GTCTCCAACCTTTCACCCCC 60.251 60.000 0.00 0.00 0.00 5.40
2115 2249 0.251209 GGTCTCCAACCTTTCACCCC 60.251 60.000 0.00 0.00 45.45 4.95
2116 2250 3.341263 GGTCTCCAACCTTTCACCC 57.659 57.895 0.00 0.00 45.45 4.61
2125 2259 1.639298 GCAGCGTCATGGTCTCCAAC 61.639 60.000 0.00 0.00 36.95 3.77
2126 2260 1.375908 GCAGCGTCATGGTCTCCAA 60.376 57.895 0.00 0.00 36.95 3.53
2127 2261 2.265739 GCAGCGTCATGGTCTCCA 59.734 61.111 0.00 0.00 38.19 3.86
2128 2262 1.812922 CTGCAGCGTCATGGTCTCC 60.813 63.158 0.00 0.00 0.00 3.71
2129 2263 1.079543 ACTGCAGCGTCATGGTCTC 60.080 57.895 15.27 0.00 0.00 3.36
2179 2313 7.933577 TCTCAGTATTTGTCTCATTTTCACTGT 59.066 33.333 0.00 0.00 34.08 3.55
2195 2329 5.669477 GCTCACATCTTCCTCTCAGTATTT 58.331 41.667 0.00 0.00 0.00 1.40
2208 2384 1.446792 CCTCACGCGCTCACATCTT 60.447 57.895 5.73 0.00 0.00 2.40
2212 2388 2.355837 GAACCTCACGCGCTCACA 60.356 61.111 5.73 0.00 0.00 3.58
2245 2421 9.939424 AGATTACTACTAGTCAAAGGATTAGGT 57.061 33.333 0.00 0.00 37.59 3.08
2265 2479 5.023452 AGGGGTCCCAAAATCAAAGATTAC 58.977 41.667 10.98 0.00 38.92 1.89
2268 2482 3.852858 AGGGGTCCCAAAATCAAAGAT 57.147 42.857 10.98 0.00 38.92 2.40
2274 2488 3.380320 CGAATTGTAGGGGTCCCAAAATC 59.620 47.826 10.98 0.56 38.92 2.17
2283 2497 1.632965 GGCCTCCGAATTGTAGGGGT 61.633 60.000 0.00 0.00 0.00 4.95
2290 2504 2.409870 GCACAGGGCCTCCGAATTG 61.410 63.158 0.95 0.00 38.33 2.32
2389 2603 1.297893 GCGTGGCGATCAATGAAGC 60.298 57.895 5.67 5.67 0.00 3.86
2407 2621 4.544689 CTCGAGCGAGCGACCAGG 62.545 72.222 6.99 0.00 36.17 4.45
2452 2666 1.393539 CGGAGGTGAAACAACGCTATG 59.606 52.381 0.00 0.00 39.98 2.23
2454 2668 0.390124 ACGGAGGTGAAACAACGCTA 59.610 50.000 0.00 0.00 39.98 4.26
2458 2672 3.982576 ATTCAACGGAGGTGAAACAAC 57.017 42.857 4.54 0.00 39.98 3.32
2502 2727 7.630242 TCTCAGAATTTCCATTTAGCGAATT 57.370 32.000 0.00 0.00 0.00 2.17
2503 2728 7.630242 TTCTCAGAATTTCCATTTAGCGAAT 57.370 32.000 0.00 0.00 0.00 3.34
2505 2730 7.630242 ATTTCTCAGAATTTCCATTTAGCGA 57.370 32.000 0.00 0.00 0.00 4.93
2506 2731 9.787532 TTTATTTCTCAGAATTTCCATTTAGCG 57.212 29.630 0.00 0.00 0.00 4.26
2573 2798 9.702494 GAGTTCTCTTCCAAATTTGATGATTTT 57.298 29.630 19.86 0.00 0.00 1.82
2574 2799 8.309656 GGAGTTCTCTTCCAAATTTGATGATTT 58.690 33.333 19.86 0.00 0.00 2.17
2575 2800 7.673082 AGGAGTTCTCTTCCAAATTTGATGATT 59.327 33.333 19.86 2.68 0.00 2.57
2576 2801 7.180663 AGGAGTTCTCTTCCAAATTTGATGAT 58.819 34.615 19.86 0.28 0.00 2.45
2577 2802 6.546484 AGGAGTTCTCTTCCAAATTTGATGA 58.454 36.000 19.86 12.31 0.00 2.92
2578 2803 6.432162 TGAGGAGTTCTCTTCCAAATTTGATG 59.568 38.462 19.86 8.86 42.86 3.07
2579 2804 6.546484 TGAGGAGTTCTCTTCCAAATTTGAT 58.454 36.000 19.86 0.00 42.86 2.57
2580 2805 5.940617 TGAGGAGTTCTCTTCCAAATTTGA 58.059 37.500 19.86 3.14 42.86 2.69
2581 2806 6.639632 TTGAGGAGTTCTCTTCCAAATTTG 57.360 37.500 11.40 11.40 42.86 2.32
2582 2807 7.846101 ATTTGAGGAGTTCTCTTCCAAATTT 57.154 32.000 0.00 0.00 42.86 1.82
2594 2819 9.912634 TGAATATGTTTCAAATTTGAGGAGTTC 57.087 29.630 19.64 18.06 38.61 3.01
2706 2931 9.935241 TTCAAATCCGATGAAAATTTTCCAATA 57.065 25.926 24.51 9.38 36.36 1.90
2707 2932 8.845413 TTCAAATCCGATGAAAATTTTCCAAT 57.155 26.923 24.51 14.33 36.36 3.16
2816 3041 9.558648 GAACTTTTTCAAAATGCATGAACTTTT 57.441 25.926 0.00 0.00 36.57 2.27
2817 3042 8.728833 TGAACTTTTTCAAAATGCATGAACTTT 58.271 25.926 0.00 0.00 38.87 2.66
2818 3043 8.266392 TGAACTTTTTCAAAATGCATGAACTT 57.734 26.923 0.00 0.00 38.87 2.66
2819 3044 7.846644 TGAACTTTTTCAAAATGCATGAACT 57.153 28.000 0.00 0.00 38.87 3.01
2820 3045 7.528182 CGATGAACTTTTTCAAAATGCATGAAC 59.472 33.333 0.00 0.00 45.01 3.18
2822 3047 6.145858 CCGATGAACTTTTTCAAAATGCATGA 59.854 34.615 0.00 0.00 45.01 3.07
2823 3048 6.145858 TCCGATGAACTTTTTCAAAATGCATG 59.854 34.615 0.00 0.00 45.01 4.06
2824 3049 6.222389 TCCGATGAACTTTTTCAAAATGCAT 58.778 32.000 0.00 0.00 45.01 3.96
2825 3050 5.595885 TCCGATGAACTTTTTCAAAATGCA 58.404 33.333 0.00 0.00 45.01 3.96
2826 3051 6.710692 ATCCGATGAACTTTTTCAAAATGC 57.289 33.333 0.00 0.00 45.01 3.56
2827 3052 8.763356 TCAAATCCGATGAACTTTTTCAAAATG 58.237 29.630 0.00 0.00 45.01 2.32
2828 3053 8.885494 TCAAATCCGATGAACTTTTTCAAAAT 57.115 26.923 0.00 0.00 45.01 1.82
2829 3054 8.709386 TTCAAATCCGATGAACTTTTTCAAAA 57.291 26.923 0.00 0.00 45.01 2.44
2830 3055 8.709386 TTTCAAATCCGATGAACTTTTTCAAA 57.291 26.923 0.00 0.00 45.01 2.69
2831 3056 8.709386 TTTTCAAATCCGATGAACTTTTTCAA 57.291 26.923 0.00 0.00 45.01 2.69
2832 3057 8.709386 TTTTTCAAATCCGATGAACTTTTTCA 57.291 26.923 0.00 0.00 45.93 2.69
2874 3099 6.648879 TTTCTCAAATCCGATGGACTTTTT 57.351 33.333 0.00 0.00 32.98 1.94
2875 3100 6.648879 TTTTCTCAAATCCGATGGACTTTT 57.351 33.333 0.00 0.00 32.98 2.27
2876 3101 6.265422 ACTTTTTCTCAAATCCGATGGACTTT 59.735 34.615 0.00 0.00 32.98 2.66
2877 3102 5.770162 ACTTTTTCTCAAATCCGATGGACTT 59.230 36.000 0.00 0.00 32.98 3.01
2878 3103 5.316987 ACTTTTTCTCAAATCCGATGGACT 58.683 37.500 0.00 0.00 32.98 3.85
2879 3104 5.629079 ACTTTTTCTCAAATCCGATGGAC 57.371 39.130 0.00 0.00 32.98 4.02
2880 3105 5.106712 CGAACTTTTTCTCAAATCCGATGGA 60.107 40.000 0.00 0.00 35.55 3.41
2881 3106 5.088739 CGAACTTTTTCTCAAATCCGATGG 58.911 41.667 0.00 0.00 0.00 3.51
2882 3107 5.927030 TCGAACTTTTTCTCAAATCCGATG 58.073 37.500 0.00 0.00 0.00 3.84
2883 3108 6.743575 ATCGAACTTTTTCTCAAATCCGAT 57.256 33.333 0.00 0.00 0.00 4.18
2884 3109 6.554334 AATCGAACTTTTTCTCAAATCCGA 57.446 33.333 0.00 0.00 0.00 4.55
2885 3110 7.623268 AAAATCGAACTTTTTCTCAAATCCG 57.377 32.000 0.00 0.00 0.00 4.18
2942 3206 9.881529 ATTGATGAAATTTTTCCAAAATCAACG 57.118 25.926 13.97 0.00 38.02 4.10


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

AutoCloner maintained by Alex Coulton.