Multiple sequence alignment - TraesCS3B01G245400

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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 TraesCS3B01G245400 chr3B 100.000 3554 0 0 1 3554 389265713 389262160 0.000000e+00 6564.0
1 TraesCS3B01G245400 chr3B 83.655 881 69 30 66 903 650840711 650839863 0.000000e+00 760.0
2 TraesCS3B01G245400 chr3B 91.667 60 3 1 1966 2025 5951316 5951373 8.180000e-12 82.4
3 TraesCS3B01G245400 chr3A 92.716 1112 37 12 905 1984 392804316 392803217 0.000000e+00 1565.0
4 TraesCS3B01G245400 chr3A 97.033 910 25 2 2067 2974 392803096 392802187 0.000000e+00 1530.0
5 TraesCS3B01G245400 chr3A 98.124 533 10 0 3022 3554 392802208 392801676 0.000000e+00 929.0
6 TraesCS3B01G245400 chr3A 86.552 699 58 19 243 914 447509921 447509232 0.000000e+00 737.0
7 TraesCS3B01G245400 chr3A 100.000 30 0 0 2022 2051 392803074 392803045 4.960000e-04 56.5
8 TraesCS3B01G245400 chr3D 92.529 1111 40 9 905 1984 295145469 295144371 0.000000e+00 1552.0
9 TraesCS3B01G245400 chr3D 95.254 885 26 7 2104 2974 295144371 295143489 0.000000e+00 1387.0
10 TraesCS3B01G245400 chr3D 93.390 711 33 6 203 906 570047475 570046772 0.000000e+00 1040.0
11 TraesCS3B01G245400 chr3D 92.958 710 36 6 203 905 54344593 54343891 0.000000e+00 1022.0
12 TraesCS3B01G245400 chr3D 97.561 533 13 0 3022 3554 295143510 295142978 0.000000e+00 913.0
13 TraesCS3B01G245400 chr3D 95.755 212 7 2 1 212 54344825 54344616 1.220000e-89 340.0
14 TraesCS3B01G245400 chr3D 95.283 212 8 2 1 212 570047707 570047498 5.690000e-88 335.0
15 TraesCS3B01G245400 chr4D 92.877 702 36 6 203 897 278384915 278384221 0.000000e+00 1007.0
16 TraesCS3B01G245400 chr4D 94.811 212 6 4 1 212 278385144 278384938 3.420000e-85 326.0
17 TraesCS3B01G245400 chr2A 84.073 879 67 29 66 903 41587938 41588784 0.000000e+00 780.0
18 TraesCS3B01G245400 chr2A 93.103 58 1 3 1975 2032 394759744 394759690 8.180000e-12 82.4
19 TraesCS3B01G245400 chr2A 96.078 51 1 1 1975 2025 406450444 406450493 8.180000e-12 82.4
20 TraesCS3B01G245400 chr7B 83.732 879 70 30 66 903 688746475 688747321 0.000000e+00 763.0
21 TraesCS3B01G245400 chr4A 86.695 699 57 19 243 914 372314278 372313589 0.000000e+00 743.0
22 TraesCS3B01G245400 chr2B 85.673 691 63 19 243 905 595162444 595163126 0.000000e+00 695.0
23 TraesCS3B01G245400 chr2B 97.826 46 1 0 1981 2026 372955399 372955354 2.940000e-11 80.5
24 TraesCS3B01G245400 chrUn 94.937 158 8 0 748 905 117285912 117285755 7.620000e-62 248.0
25 TraesCS3B01G245400 chr5B 94.937 158 8 0 748 905 581763995 581763838 7.620000e-62 248.0
26 TraesCS3B01G245400 chr5B 94.304 158 9 0 748 905 420935839 420935682 3.540000e-60 243.0
27 TraesCS3B01G245400 chr5B 86.111 72 7 3 1957 2025 180913284 180913355 1.370000e-09 75.0
28 TraesCS3B01G245400 chr4B 100.000 47 0 0 1979 2025 43788386 43788340 1.760000e-13 87.9
29 TraesCS3B01G245400 chr4B 96.226 53 2 0 1973 2025 296169164 296169216 1.760000e-13 87.9
30 TraesCS3B01G245400 chr2D 94.643 56 0 3 1971 2025 7661714 7661661 2.270000e-12 84.2
31 TraesCS3B01G245400 chr6B 92.727 55 4 0 1971 2025 651412741 651412687 2.940000e-11 80.5


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 TraesCS3B01G245400 chr3B 389262160 389265713 3553 True 6564.000 6564 100.000000 1 3554 1 chr3B.!!$R1 3553
1 TraesCS3B01G245400 chr3B 650839863 650840711 848 True 760.000 760 83.655000 66 903 1 chr3B.!!$R2 837
2 TraesCS3B01G245400 chr3A 392801676 392804316 2640 True 1020.125 1565 96.968250 905 3554 4 chr3A.!!$R2 2649
3 TraesCS3B01G245400 chr3A 447509232 447509921 689 True 737.000 737 86.552000 243 914 1 chr3A.!!$R1 671
4 TraesCS3B01G245400 chr3D 295142978 295145469 2491 True 1284.000 1552 95.114667 905 3554 3 chr3D.!!$R2 2649
5 TraesCS3B01G245400 chr3D 570046772 570047707 935 True 687.500 1040 94.336500 1 906 2 chr3D.!!$R3 905
6 TraesCS3B01G245400 chr3D 54343891 54344825 934 True 681.000 1022 94.356500 1 905 2 chr3D.!!$R1 904
7 TraesCS3B01G245400 chr4D 278384221 278385144 923 True 666.500 1007 93.844000 1 897 2 chr4D.!!$R1 896
8 TraesCS3B01G245400 chr2A 41587938 41588784 846 False 780.000 780 84.073000 66 903 1 chr2A.!!$F1 837
9 TraesCS3B01G245400 chr7B 688746475 688747321 846 False 763.000 763 83.732000 66 903 1 chr7B.!!$F1 837
10 TraesCS3B01G245400 chr4A 372313589 372314278 689 True 743.000 743 86.695000 243 914 1 chr4A.!!$R1 671
11 TraesCS3B01G245400 chr2B 595162444 595163126 682 False 695.000 695 85.673000 243 905 1 chr2B.!!$F1 662

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
357 411 0.036022 AGAGAAGGCACAGCTTGGAC 59.964 55.000 0.00 0.00 0.00 4.02 F
1126 1214 0.029433 GGCTGCGGCTGCTATAAAAC 59.971 55.000 27.14 8.68 43.34 2.43 F
1455 1572 1.003580 TGAGGCCTTGATGTCTTCCAC 59.996 52.381 6.77 0.00 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1641 1759 0.036164 CCACCGTCAAGATCCAACCA 59.964 55.000 0.0 0.0 0.0 3.67 R
2268 2495 1.148498 GCAGTAATCCCCCTTCCCG 59.852 63.158 0.0 0.0 0.0 5.14 R
2679 2907 1.811965 TGCAGAAAATCCACCGACATG 59.188 47.619 0.0 0.0 0.0 3.21 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
44 45 4.245660 CTGATTCAGACAAGGCGAGTAAA 58.754 43.478 8.00 0.00 32.44 2.01
199 204 0.659957 GCATCTAGCGGCAAAAGGAG 59.340 55.000 1.45 0.00 0.00 3.69
240 276 1.127766 CGCGCTGCACAACTACAAATA 59.872 47.619 5.56 0.00 0.00 1.40
299 342 2.772568 TTGGCTGTGTTTTGTCATCG 57.227 45.000 0.00 0.00 0.00 3.84
307 350 3.996363 TGTGTTTTGTCATCGATCTCCTG 59.004 43.478 0.00 0.00 0.00 3.86
330 380 1.832912 CAAGAATCCGAGGAGGGGG 59.167 63.158 0.00 0.00 41.52 5.40
337 387 1.534235 CCGAGGAGGGGGTATCTGG 60.534 68.421 0.00 0.00 35.97 3.86
338 388 1.542175 CGAGGAGGGGGTATCTGGA 59.458 63.158 0.00 0.00 0.00 3.86
349 399 2.111384 GGTATCTGGAGAGAAGGCACA 58.889 52.381 0.00 0.00 0.00 4.57
357 411 0.036022 AGAGAAGGCACAGCTTGGAC 59.964 55.000 0.00 0.00 0.00 4.02
440 507 3.895041 TGGTATTCCATGAGCTGTCGATA 59.105 43.478 0.00 0.00 39.03 2.92
526 595 2.574322 GACATGCTGCACACGTTTTAG 58.426 47.619 3.57 0.00 0.00 1.85
641 715 5.980116 CAGACCTAGGATTTAGTTCATGTCG 59.020 44.000 17.98 0.00 0.00 4.35
642 716 5.657302 AGACCTAGGATTTAGTTCATGTCGT 59.343 40.000 17.98 0.00 0.00 4.34
643 717 5.661458 ACCTAGGATTTAGTTCATGTCGTG 58.339 41.667 17.98 0.00 0.00 4.35
730 806 8.311395 TCTTATGGACACATGAGAACTTATCT 57.689 34.615 0.00 0.00 44.01 1.98
798 876 9.877137 GAAACGTATGTGCATAAATTGATATCA 57.123 29.630 0.00 0.00 0.00 2.15
802 880 9.533983 CGTATGTGCATAAATTGATATCAGAAC 57.466 33.333 5.39 0.00 0.00 3.01
931 1016 6.451064 AATAAACTTTCCGATGAACCATCC 57.549 37.500 0.00 0.00 37.57 3.51
932 1017 2.420058 ACTTTCCGATGAACCATCCC 57.580 50.000 0.00 0.00 37.57 3.85
989 1074 1.959042 AAGGCAGCCAATCGAGTATG 58.041 50.000 15.80 0.00 0.00 2.39
990 1075 0.533755 AGGCAGCCAATCGAGTATGC 60.534 55.000 15.80 7.99 0.00 3.14
1031 1116 0.889186 AGGGCGAACAAAGCGAATGT 60.889 50.000 0.00 0.00 35.00 2.71
1036 1121 2.334454 GCGAACAAAGCGAATGTAAACG 59.666 45.455 0.00 0.00 0.00 3.60
1054 1142 1.633852 CGCAAGCACAAGAGAGAGGC 61.634 60.000 0.00 0.00 0.00 4.70
1126 1214 0.029433 GGCTGCGGCTGCTATAAAAC 59.971 55.000 27.14 8.68 43.34 2.43
1189 1277 2.099831 CACGCCGGAGTCTCGTAC 59.900 66.667 8.30 0.00 34.81 3.67
1455 1572 1.003580 TGAGGCCTTGATGTCTTCCAC 59.996 52.381 6.77 0.00 0.00 4.02
1456 1573 1.280421 GAGGCCTTGATGTCTTCCACT 59.720 52.381 6.77 0.00 0.00 4.00
1457 1574 1.707427 AGGCCTTGATGTCTTCCACTT 59.293 47.619 0.00 0.00 0.00 3.16
1458 1575 2.087646 GGCCTTGATGTCTTCCACTTC 58.912 52.381 0.00 0.00 0.00 3.01
1459 1576 2.087646 GCCTTGATGTCTTCCACTTCC 58.912 52.381 0.00 0.00 0.00 3.46
1460 1577 2.553028 GCCTTGATGTCTTCCACTTCCA 60.553 50.000 0.00 0.00 0.00 3.53
1602 1719 2.106511 AGGGTATGAAATGGACCGATGG 59.893 50.000 0.00 0.00 33.77 3.51
1884 2008 3.749226 TGACAACATGTGCAAGGTATGA 58.251 40.909 0.00 0.00 0.00 2.15
1904 2028 3.118629 TGAACAGTAGGATGGCAGATCAC 60.119 47.826 0.00 0.00 0.00 3.06
1909 2033 3.972638 AGTAGGATGGCAGATCACTTCAT 59.027 43.478 0.00 0.00 0.00 2.57
1917 2041 5.255687 TGGCAGATCACTTCATGTGTTAAT 58.744 37.500 0.00 0.00 46.27 1.40
1992 2118 7.941431 ATTCACTTAGTATATACTCCCTCCG 57.059 40.000 18.68 4.94 37.73 4.63
1993 2119 6.445451 TCACTTAGTATATACTCCCTCCGT 57.555 41.667 18.68 5.91 37.73 4.69
1994 2120 6.471146 TCACTTAGTATATACTCCCTCCGTC 58.529 44.000 18.68 0.00 37.73 4.79
1995 2121 6.271857 TCACTTAGTATATACTCCCTCCGTCT 59.728 42.308 18.68 0.00 37.73 4.18
1996 2122 6.594937 CACTTAGTATATACTCCCTCCGTCTC 59.405 46.154 18.68 0.00 37.73 3.36
1997 2123 6.271857 ACTTAGTATATACTCCCTCCGTCTCA 59.728 42.308 18.68 0.00 37.73 3.27
1998 2124 5.579753 AGTATATACTCCCTCCGTCTCAA 57.420 43.478 9.71 0.00 0.00 3.02
1999 2125 5.950023 AGTATATACTCCCTCCGTCTCAAA 58.050 41.667 9.71 0.00 0.00 2.69
2000 2126 6.371278 AGTATATACTCCCTCCGTCTCAAAA 58.629 40.000 9.71 0.00 0.00 2.44
2001 2127 7.011382 AGTATATACTCCCTCCGTCTCAAAAT 58.989 38.462 9.71 0.00 0.00 1.82
2002 2128 8.168725 AGTATATACTCCCTCCGTCTCAAAATA 58.831 37.037 9.71 0.00 0.00 1.40
2003 2129 7.850935 ATATACTCCCTCCGTCTCAAAATAA 57.149 36.000 0.00 0.00 0.00 1.40
2004 2130 4.473477 ACTCCCTCCGTCTCAAAATAAG 57.527 45.455 0.00 0.00 0.00 1.73
2005 2131 3.838903 ACTCCCTCCGTCTCAAAATAAGT 59.161 43.478 0.00 0.00 0.00 2.24
2006 2132 4.184629 CTCCCTCCGTCTCAAAATAAGTG 58.815 47.826 0.00 0.00 0.00 3.16
2007 2133 3.581332 TCCCTCCGTCTCAAAATAAGTGT 59.419 43.478 0.00 0.00 0.00 3.55
2008 2134 3.933332 CCCTCCGTCTCAAAATAAGTGTC 59.067 47.826 0.00 0.00 0.00 3.67
2009 2135 4.322801 CCCTCCGTCTCAAAATAAGTGTCT 60.323 45.833 0.00 0.00 0.00 3.41
2010 2136 5.238583 CCTCCGTCTCAAAATAAGTGTCTT 58.761 41.667 0.00 0.00 0.00 3.01
2011 2137 5.120830 CCTCCGTCTCAAAATAAGTGTCTTG 59.879 44.000 0.00 0.00 0.00 3.02
2012 2138 5.849510 TCCGTCTCAAAATAAGTGTCTTGA 58.150 37.500 0.00 0.00 0.00 3.02
2013 2139 5.926542 TCCGTCTCAAAATAAGTGTCTTGAG 59.073 40.000 4.63 4.63 43.97 3.02
2014 2140 5.389935 CCGTCTCAAAATAAGTGTCTTGAGC 60.390 44.000 5.91 1.95 42.87 4.26
2015 2141 5.406780 CGTCTCAAAATAAGTGTCTTGAGCT 59.593 40.000 5.91 0.00 42.87 4.09
2016 2142 6.073548 CGTCTCAAAATAAGTGTCTTGAGCTT 60.074 38.462 5.91 0.00 42.87 3.74
2017 2143 7.116376 CGTCTCAAAATAAGTGTCTTGAGCTTA 59.884 37.037 5.91 0.00 42.87 3.09
2018 2144 8.439286 GTCTCAAAATAAGTGTCTTGAGCTTAG 58.561 37.037 5.91 0.00 42.87 2.18
2019 2145 8.150945 TCTCAAAATAAGTGTCTTGAGCTTAGT 58.849 33.333 5.91 0.00 42.87 2.24
2020 2146 9.424319 CTCAAAATAAGTGTCTTGAGCTTAGTA 57.576 33.333 0.00 0.00 38.63 1.82
2021 2147 9.204570 TCAAAATAAGTGTCTTGAGCTTAGTAC 57.795 33.333 0.00 0.00 0.00 2.73
2022 2148 8.988934 CAAAATAAGTGTCTTGAGCTTAGTACA 58.011 33.333 0.00 0.00 0.00 2.90
2023 2149 9.555727 AAAATAAGTGTCTTGAGCTTAGTACAA 57.444 29.630 0.00 0.00 0.00 2.41
2024 2150 9.555727 AAATAAGTGTCTTGAGCTTAGTACAAA 57.444 29.630 0.00 0.00 0.00 2.83
2025 2151 6.846325 AAGTGTCTTGAGCTTAGTACAAAC 57.154 37.500 0.00 0.00 0.00 2.93
2026 2152 4.982916 AGTGTCTTGAGCTTAGTACAAACG 59.017 41.667 0.00 0.00 0.00 3.60
2027 2153 4.980434 GTGTCTTGAGCTTAGTACAAACGA 59.020 41.667 0.00 0.00 0.00 3.85
2028 2154 5.634020 GTGTCTTGAGCTTAGTACAAACGAT 59.366 40.000 0.00 0.00 0.00 3.73
2029 2155 6.145696 GTGTCTTGAGCTTAGTACAAACGATT 59.854 38.462 0.00 0.00 0.00 3.34
2030 2156 6.145534 TGTCTTGAGCTTAGTACAAACGATTG 59.854 38.462 3.59 3.59 42.46 2.67
2031 2157 6.365247 GTCTTGAGCTTAGTACAAACGATTGA 59.635 38.462 12.79 0.00 38.94 2.57
2032 2158 7.063544 GTCTTGAGCTTAGTACAAACGATTGAT 59.936 37.037 12.79 0.62 38.94 2.57
2033 2159 8.248253 TCTTGAGCTTAGTACAAACGATTGATA 58.752 33.333 12.79 0.00 38.94 2.15
2034 2160 8.766000 TTGAGCTTAGTACAAACGATTGATAA 57.234 30.769 12.79 7.22 38.94 1.75
2035 2161 8.766000 TGAGCTTAGTACAAACGATTGATAAA 57.234 30.769 12.79 0.72 38.94 1.40
2036 2162 9.210329 TGAGCTTAGTACAAACGATTGATAAAA 57.790 29.630 12.79 1.04 38.94 1.52
2059 2185 4.852134 ATTGTGTGTGCTGCATTTAGAA 57.148 36.364 5.27 0.38 0.00 2.10
2064 2190 4.855388 GTGTGTGCTGCATTTAGAATCTTG 59.145 41.667 5.27 0.00 0.00 3.02
2065 2191 4.520111 TGTGTGCTGCATTTAGAATCTTGT 59.480 37.500 5.27 0.00 0.00 3.16
2093 2309 4.989279 AGGCATGATGTATTGTCAAACC 57.011 40.909 0.00 0.00 0.00 3.27
2165 2390 3.564053 AAGTGGTGAAAACCGACCTTA 57.436 42.857 0.00 0.00 32.98 2.69
2268 2495 4.621991 AGCACTTCATATACATCGGTGAC 58.378 43.478 0.65 0.00 0.00 3.67
2592 2819 2.699954 CTCACGGTACAGGCAAGATTT 58.300 47.619 0.00 0.00 0.00 2.17
2679 2907 5.049398 TGTAACAAATAATTGCACCGACC 57.951 39.130 0.00 0.00 40.34 4.79
2715 2943 7.977789 TTTTCTGCACATTGTGTCTCTTATA 57.022 32.000 17.64 0.00 35.75 0.98
2793 3021 1.352622 ACAGGCAAGTTCAGGGACCA 61.353 55.000 0.00 0.00 0.00 4.02
2968 3196 1.786937 CCAGCTCCTGGTCTCATAGT 58.213 55.000 3.09 0.00 45.82 2.12
2969 3197 2.114616 CCAGCTCCTGGTCTCATAGTT 58.885 52.381 3.09 0.00 45.82 2.24
2970 3198 2.503356 CCAGCTCCTGGTCTCATAGTTT 59.497 50.000 3.09 0.00 45.82 2.66
2971 3199 3.054802 CCAGCTCCTGGTCTCATAGTTTT 60.055 47.826 3.09 0.00 45.82 2.43
2972 3200 3.937706 CAGCTCCTGGTCTCATAGTTTTG 59.062 47.826 0.00 0.00 0.00 2.44
2973 3201 3.584848 AGCTCCTGGTCTCATAGTTTTGT 59.415 43.478 0.00 0.00 0.00 2.83
2974 3202 4.042187 AGCTCCTGGTCTCATAGTTTTGTT 59.958 41.667 0.00 0.00 0.00 2.83
2975 3203 4.762251 GCTCCTGGTCTCATAGTTTTGTTT 59.238 41.667 0.00 0.00 0.00 2.83
2976 3204 5.241728 GCTCCTGGTCTCATAGTTTTGTTTT 59.758 40.000 0.00 0.00 0.00 2.43
2977 3205 6.633500 TCCTGGTCTCATAGTTTTGTTTTG 57.367 37.500 0.00 0.00 0.00 2.44
2978 3206 6.126409 TCCTGGTCTCATAGTTTTGTTTTGT 58.874 36.000 0.00 0.00 0.00 2.83
2979 3207 6.605594 TCCTGGTCTCATAGTTTTGTTTTGTT 59.394 34.615 0.00 0.00 0.00 2.83
2980 3208 7.123547 TCCTGGTCTCATAGTTTTGTTTTGTTT 59.876 33.333 0.00 0.00 0.00 2.83
2981 3209 7.763985 CCTGGTCTCATAGTTTTGTTTTGTTTT 59.236 33.333 0.00 0.00 0.00 2.43
2982 3210 9.150348 CTGGTCTCATAGTTTTGTTTTGTTTTT 57.850 29.630 0.00 0.00 0.00 1.94
3004 3232 3.611766 TTTTTGCGGGAAAAACCTTCA 57.388 38.095 14.93 0.00 38.38 3.02
3005 3233 3.611766 TTTTGCGGGAAAAACCTTCAA 57.388 38.095 4.86 0.00 38.98 2.69
3006 3234 3.828875 TTTGCGGGAAAAACCTTCAAT 57.171 38.095 0.00 0.00 38.98 2.57
3007 3235 3.378911 TTGCGGGAAAAACCTTCAATC 57.621 42.857 0.00 0.00 38.98 2.67
3008 3236 2.593026 TGCGGGAAAAACCTTCAATCT 58.407 42.857 0.00 0.00 38.98 2.40
3009 3237 3.757270 TGCGGGAAAAACCTTCAATCTA 58.243 40.909 0.00 0.00 38.98 1.98
3010 3238 4.340617 TGCGGGAAAAACCTTCAATCTAT 58.659 39.130 0.00 0.00 38.98 1.98
3011 3239 4.770010 TGCGGGAAAAACCTTCAATCTATT 59.230 37.500 0.00 0.00 38.98 1.73
3012 3240 5.105917 TGCGGGAAAAACCTTCAATCTATTC 60.106 40.000 0.00 0.00 38.98 1.75
3013 3241 5.105917 GCGGGAAAAACCTTCAATCTATTCA 60.106 40.000 0.00 0.00 38.98 2.57
3014 3242 6.405842 GCGGGAAAAACCTTCAATCTATTCAT 60.406 38.462 0.00 0.00 38.98 2.57
3015 3243 7.196331 CGGGAAAAACCTTCAATCTATTCATC 58.804 38.462 0.00 0.00 38.98 2.92
3016 3244 7.196331 GGGAAAAACCTTCAATCTATTCATCG 58.804 38.462 0.00 0.00 38.98 3.84
3017 3245 7.148069 GGGAAAAACCTTCAATCTATTCATCGT 60.148 37.037 0.00 0.00 38.98 3.73
3018 3246 7.910683 GGAAAAACCTTCAATCTATTCATCGTC 59.089 37.037 0.00 0.00 35.41 4.20
3019 3247 7.921786 AAAACCTTCAATCTATTCATCGTCA 57.078 32.000 0.00 0.00 0.00 4.35
3020 3248 6.910536 AACCTTCAATCTATTCATCGTCAC 57.089 37.500 0.00 0.00 0.00 3.67
3021 3249 5.360591 ACCTTCAATCTATTCATCGTCACC 58.639 41.667 0.00 0.00 0.00 4.02
3022 3250 5.129485 ACCTTCAATCTATTCATCGTCACCT 59.871 40.000 0.00 0.00 0.00 4.00
3023 3251 5.694006 CCTTCAATCTATTCATCGTCACCTC 59.306 44.000 0.00 0.00 0.00 3.85
3024 3252 5.201713 TCAATCTATTCATCGTCACCTCC 57.798 43.478 0.00 0.00 0.00 4.30
3025 3253 4.895889 TCAATCTATTCATCGTCACCTCCT 59.104 41.667 0.00 0.00 0.00 3.69
3026 3254 4.862902 ATCTATTCATCGTCACCTCCTG 57.137 45.455 0.00 0.00 0.00 3.86
3046 3274 7.233553 CCTCCTGGTCTCATAGTTTATGTATGA 59.766 40.741 0.00 0.00 37.45 2.15
3318 3546 7.094634 GGATCTAACTCAAACAATCTTTCTGCA 60.095 37.037 0.00 0.00 0.00 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
88 89 3.118811 TCATCTCCATGCATGTTGTACGA 60.119 43.478 24.58 12.58 0.00 3.43
199 204 0.104671 CAAGAGCCCTAGAGAGCTGC 59.895 60.000 6.62 0.00 40.11 5.25
240 276 4.501058 GGAGAGAAAGAAACACGTACCTGT 60.501 45.833 0.00 0.00 0.00 4.00
299 342 3.497640 CGGATTCTTGCAATCAGGAGATC 59.502 47.826 0.00 0.81 31.90 2.75
307 350 2.216898 CCTCCTCGGATTCTTGCAATC 58.783 52.381 0.00 0.00 33.16 2.67
330 380 2.482839 GCTGTGCCTTCTCTCCAGATAC 60.483 54.545 0.00 0.00 0.00 2.24
337 387 0.322975 TCCAAGCTGTGCCTTCTCTC 59.677 55.000 0.00 0.00 0.00 3.20
338 388 0.036022 GTCCAAGCTGTGCCTTCTCT 59.964 55.000 0.00 0.00 0.00 3.10
349 399 1.202330 CCTCTCCAGATGTCCAAGCT 58.798 55.000 0.00 0.00 0.00 3.74
357 411 1.070445 CCTAAGCAGCCTCTCCAGATG 59.930 57.143 0.00 0.00 0.00 2.90
440 507 5.596836 TGGAAGACAATTTTCTGCAACTT 57.403 34.783 2.01 0.00 0.00 2.66
526 595 3.058639 GGAATGGAAATCTGCTATGTCGC 60.059 47.826 0.00 0.00 0.00 5.19
641 715 2.017049 CTAGGCATACCCACAAAGCAC 58.983 52.381 0.00 0.00 36.11 4.40
642 716 1.064758 CCTAGGCATACCCACAAAGCA 60.065 52.381 0.00 0.00 36.11 3.91
643 717 1.211949 TCCTAGGCATACCCACAAAGC 59.788 52.381 2.96 0.00 36.11 3.51
776 852 9.533983 GTTCTGATATCAATTTATGCACATACG 57.466 33.333 6.90 0.00 0.00 3.06
798 876 8.383175 TCCCACATCTTAAACTTTGATAGTTCT 58.617 33.333 0.00 0.00 46.34 3.01
918 1003 1.618837 ACGATAGGGATGGTTCATCGG 59.381 52.381 7.14 0.00 42.02 4.18
931 1016 2.609459 GGTGCTTTGTCATCACGATAGG 59.391 50.000 0.00 0.00 43.77 2.57
932 1017 3.261580 TGGTGCTTTGTCATCACGATAG 58.738 45.455 0.00 0.00 46.19 2.08
989 1074 1.129811 GCCGTACCATAACTGTTGTGC 59.870 52.381 11.29 0.42 0.00 4.57
990 1075 1.392168 CGCCGTACCATAACTGTTGTG 59.608 52.381 9.97 9.97 0.00 3.33
1031 1116 3.059884 CTCTCTCTTGTGCTTGCGTTTA 58.940 45.455 0.00 0.00 0.00 2.01
1036 1121 1.304509 GGCCTCTCTCTTGTGCTTGC 61.305 60.000 0.00 0.00 0.00 4.01
1040 1125 0.250467 TTGTGGCCTCTCTCTTGTGC 60.250 55.000 3.32 0.00 0.00 4.57
1105 1193 2.587322 TTTATAGCAGCCGCAGCCGT 62.587 55.000 3.83 0.00 42.27 5.68
1106 1194 1.436195 TTTTATAGCAGCCGCAGCCG 61.436 55.000 3.83 0.00 42.27 5.52
1107 1195 0.029433 GTTTTATAGCAGCCGCAGCC 59.971 55.000 3.83 0.00 42.27 4.85
1108 1196 0.029433 GGTTTTATAGCAGCCGCAGC 59.971 55.000 0.00 0.00 42.27 5.25
1109 1197 1.064060 GTGGTTTTATAGCAGCCGCAG 59.936 52.381 0.00 0.00 42.27 5.18
1110 1198 1.091537 GTGGTTTTATAGCAGCCGCA 58.908 50.000 0.00 0.00 42.27 5.69
1111 1199 1.091537 TGTGGTTTTATAGCAGCCGC 58.908 50.000 0.00 0.00 34.32 6.53
1112 1200 1.400494 GGTGTGGTTTTATAGCAGCCG 59.600 52.381 0.00 0.00 34.32 5.52
1126 1214 1.674651 TCTCGGACTCTCGGTGTGG 60.675 63.158 0.00 0.00 0.00 4.17
1368 1477 1.922570 ATCGTGTTCGTACCATGAGC 58.077 50.000 0.00 0.00 38.33 4.26
1455 1572 1.142465 CCCATCATCCTGTCCTGGAAG 59.858 57.143 0.00 0.00 39.85 3.46
1456 1573 1.216064 CCCATCATCCTGTCCTGGAA 58.784 55.000 0.00 0.00 39.85 3.53
1457 1574 0.695462 CCCCATCATCCTGTCCTGGA 60.695 60.000 0.00 0.00 40.82 3.86
1458 1575 1.713005 CCCCCATCATCCTGTCCTGG 61.713 65.000 0.00 0.00 0.00 4.45
1459 1576 0.695462 TCCCCCATCATCCTGTCCTG 60.695 60.000 0.00 0.00 0.00 3.86
1460 1577 0.401105 CTCCCCCATCATCCTGTCCT 60.401 60.000 0.00 0.00 0.00 3.85
1602 1719 0.447801 AGAACACATCGGCAAATCGC 59.552 50.000 0.00 0.00 41.28 4.58
1641 1759 0.036164 CCACCGTCAAGATCCAACCA 59.964 55.000 0.00 0.00 0.00 3.67
1642 1760 0.036306 ACCACCGTCAAGATCCAACC 59.964 55.000 0.00 0.00 0.00 3.77
1853 1977 0.538057 CATGTTGTCAGGGCACAGGT 60.538 55.000 0.00 0.00 0.00 4.00
1884 2008 3.110705 AGTGATCTGCCATCCTACTGTT 58.889 45.455 0.00 0.00 0.00 3.16
1909 2033 6.220201 TCGAGTGAATCTGTGAATTAACACA 58.780 36.000 0.00 0.00 46.45 3.72
1917 2041 2.995939 GTGCATCGAGTGAATCTGTGAA 59.004 45.455 0.00 0.00 0.00 3.18
1975 2101 6.692849 TTGAGACGGAGGGAGTATATACTA 57.307 41.667 15.42 0.00 36.50 1.82
1984 2110 4.184629 CACTTATTTTGAGACGGAGGGAG 58.815 47.826 0.00 0.00 0.00 4.30
1985 2111 3.581332 ACACTTATTTTGAGACGGAGGGA 59.419 43.478 0.00 0.00 0.00 4.20
1986 2112 3.933332 GACACTTATTTTGAGACGGAGGG 59.067 47.826 0.00 0.00 0.00 4.30
1988 2114 5.926542 TCAAGACACTTATTTTGAGACGGAG 59.073 40.000 0.00 0.00 0.00 4.63
1989 2115 5.849510 TCAAGACACTTATTTTGAGACGGA 58.150 37.500 0.00 0.00 0.00 4.69
1990 2116 5.389935 GCTCAAGACACTTATTTTGAGACGG 60.390 44.000 15.10 0.00 45.82 4.79
1991 2117 5.406780 AGCTCAAGACACTTATTTTGAGACG 59.593 40.000 15.10 0.00 45.82 4.18
1992 2118 6.793492 AGCTCAAGACACTTATTTTGAGAC 57.207 37.500 15.10 7.85 45.82 3.36
1993 2119 8.150945 ACTAAGCTCAAGACACTTATTTTGAGA 58.849 33.333 15.10 0.00 45.82 3.27
1994 2120 8.316640 ACTAAGCTCAAGACACTTATTTTGAG 57.683 34.615 8.33 8.33 45.75 3.02
1995 2121 9.204570 GTACTAAGCTCAAGACACTTATTTTGA 57.795 33.333 3.19 0.00 0.00 2.69
1996 2122 8.988934 TGTACTAAGCTCAAGACACTTATTTTG 58.011 33.333 3.19 0.00 0.00 2.44
1997 2123 9.555727 TTGTACTAAGCTCAAGACACTTATTTT 57.444 29.630 3.19 0.00 0.00 1.82
1998 2124 9.555727 TTTGTACTAAGCTCAAGACACTTATTT 57.444 29.630 3.19 0.00 0.00 1.40
1999 2125 8.989980 GTTTGTACTAAGCTCAAGACACTTATT 58.010 33.333 3.19 0.00 0.00 1.40
2000 2126 7.328737 CGTTTGTACTAAGCTCAAGACACTTAT 59.671 37.037 3.19 0.00 0.00 1.73
2001 2127 6.639686 CGTTTGTACTAAGCTCAAGACACTTA 59.360 38.462 3.19 0.00 0.00 2.24
2002 2128 5.462398 CGTTTGTACTAAGCTCAAGACACTT 59.538 40.000 3.19 0.00 0.00 3.16
2003 2129 4.982916 CGTTTGTACTAAGCTCAAGACACT 59.017 41.667 3.19 0.00 0.00 3.55
2004 2130 4.980434 TCGTTTGTACTAAGCTCAAGACAC 59.020 41.667 3.19 2.09 0.00 3.67
2005 2131 5.190992 TCGTTTGTACTAAGCTCAAGACA 57.809 39.130 3.19 0.00 0.00 3.41
2006 2132 6.365247 TCAATCGTTTGTACTAAGCTCAAGAC 59.635 38.462 6.14 0.00 34.32 3.01
2007 2133 6.452242 TCAATCGTTTGTACTAAGCTCAAGA 58.548 36.000 6.14 0.00 34.32 3.02
2008 2134 6.706055 TCAATCGTTTGTACTAAGCTCAAG 57.294 37.500 6.14 0.00 34.32 3.02
2009 2135 8.766000 TTATCAATCGTTTGTACTAAGCTCAA 57.234 30.769 6.14 0.00 34.32 3.02
2010 2136 8.766000 TTTATCAATCGTTTGTACTAAGCTCA 57.234 30.769 6.14 0.00 34.32 4.26
2020 2146 9.906660 ACACACAATATTTTATCAATCGTTTGT 57.093 25.926 6.14 0.00 34.32 2.83
2022 2148 8.859156 GCACACACAATATTTTATCAATCGTTT 58.141 29.630 0.00 0.00 0.00 3.60
2023 2149 8.243426 AGCACACACAATATTTTATCAATCGTT 58.757 29.630 0.00 0.00 0.00 3.85
2024 2150 7.697710 CAGCACACACAATATTTTATCAATCGT 59.302 33.333 0.00 0.00 0.00 3.73
2025 2151 7.305590 GCAGCACACACAATATTTTATCAATCG 60.306 37.037 0.00 0.00 0.00 3.34
2026 2152 7.488792 TGCAGCACACACAATATTTTATCAATC 59.511 33.333 0.00 0.00 0.00 2.67
2027 2153 7.321908 TGCAGCACACACAATATTTTATCAAT 58.678 30.769 0.00 0.00 0.00 2.57
2028 2154 6.685657 TGCAGCACACACAATATTTTATCAA 58.314 32.000 0.00 0.00 0.00 2.57
2029 2155 6.264841 TGCAGCACACACAATATTTTATCA 57.735 33.333 0.00 0.00 0.00 2.15
2030 2156 7.760131 AATGCAGCACACACAATATTTTATC 57.240 32.000 0.00 0.00 0.00 1.75
2031 2157 9.304731 CTAAATGCAGCACACACAATATTTTAT 57.695 29.630 0.00 0.00 0.00 1.40
2032 2158 8.518702 TCTAAATGCAGCACACACAATATTTTA 58.481 29.630 0.00 0.00 0.00 1.52
2033 2159 7.377398 TCTAAATGCAGCACACACAATATTTT 58.623 30.769 0.00 0.00 0.00 1.82
2034 2160 6.923012 TCTAAATGCAGCACACACAATATTT 58.077 32.000 0.00 0.00 0.00 1.40
2035 2161 6.513806 TCTAAATGCAGCACACACAATATT 57.486 33.333 0.00 0.00 0.00 1.28
2036 2162 6.513806 TTCTAAATGCAGCACACACAATAT 57.486 33.333 0.00 0.00 0.00 1.28
2037 2163 5.956068 TTCTAAATGCAGCACACACAATA 57.044 34.783 0.00 0.00 0.00 1.90
2038 2164 4.852134 TTCTAAATGCAGCACACACAAT 57.148 36.364 0.00 0.00 0.00 2.71
2039 2165 4.520111 AGATTCTAAATGCAGCACACACAA 59.480 37.500 0.00 0.00 0.00 3.33
2040 2166 4.074259 AGATTCTAAATGCAGCACACACA 58.926 39.130 0.00 0.00 0.00 3.72
2041 2167 4.691860 AGATTCTAAATGCAGCACACAC 57.308 40.909 0.00 0.00 0.00 3.82
2064 2190 9.489084 TTGACAATACATCATGCCTAATACTAC 57.511 33.333 0.00 0.00 0.00 2.73
2093 2309 8.914328 TCAGCACACACAATATTTTATCAATG 57.086 30.769 0.00 0.00 0.00 2.82
2165 2390 5.393866 AGTGAAATTTAGTTCATGGGTGGT 58.606 37.500 0.00 0.00 39.61 4.16
2225 2452 1.486310 TGTTCTTGGCACTGTCTGTCT 59.514 47.619 0.00 0.00 0.00 3.41
2268 2495 1.148498 GCAGTAATCCCCCTTCCCG 59.852 63.158 0.00 0.00 0.00 5.14
2427 2654 2.880890 CAGCTTGTTCACCAGCTTAAGT 59.119 45.455 4.02 0.00 35.17 2.24
2679 2907 1.811965 TGCAGAAAATCCACCGACATG 59.188 47.619 0.00 0.00 0.00 3.21
2705 2933 6.986817 GCTATCCTGCAGTTTTATAAGAGACA 59.013 38.462 13.81 0.00 0.00 3.41
2715 2943 3.251729 CGCATATGCTATCCTGCAGTTTT 59.748 43.478 24.56 0.00 46.71 2.43
2984 3212 3.611766 TGAAGGTTTTTCCCGCAAAAA 57.388 38.095 0.46 0.46 40.93 1.94
2985 3213 3.611766 TTGAAGGTTTTTCCCGCAAAA 57.388 38.095 0.00 0.00 36.75 2.44
2986 3214 3.386402 AGATTGAAGGTTTTTCCCGCAAA 59.614 39.130 0.00 0.00 34.83 3.68
2987 3215 2.962421 AGATTGAAGGTTTTTCCCGCAA 59.038 40.909 0.00 0.00 36.75 4.85
2988 3216 2.593026 AGATTGAAGGTTTTTCCCGCA 58.407 42.857 0.00 0.00 36.75 5.69
2989 3217 4.983671 ATAGATTGAAGGTTTTTCCCGC 57.016 40.909 0.00 0.00 36.75 6.13
2990 3218 6.509418 TGAATAGATTGAAGGTTTTTCCCG 57.491 37.500 0.00 0.00 36.75 5.14
2991 3219 7.148069 ACGATGAATAGATTGAAGGTTTTTCCC 60.148 37.037 0.00 0.00 36.75 3.97
2992 3220 7.762382 ACGATGAATAGATTGAAGGTTTTTCC 58.238 34.615 0.00 0.00 0.00 3.13
2993 3221 8.450964 TGACGATGAATAGATTGAAGGTTTTTC 58.549 33.333 0.00 0.00 0.00 2.29
2994 3222 8.237267 GTGACGATGAATAGATTGAAGGTTTTT 58.763 33.333 0.00 0.00 0.00 1.94
2995 3223 7.148239 GGTGACGATGAATAGATTGAAGGTTTT 60.148 37.037 0.00 0.00 0.00 2.43
2996 3224 6.316390 GGTGACGATGAATAGATTGAAGGTTT 59.684 38.462 0.00 0.00 0.00 3.27
2997 3225 5.817816 GGTGACGATGAATAGATTGAAGGTT 59.182 40.000 0.00 0.00 0.00 3.50
2998 3226 5.129485 AGGTGACGATGAATAGATTGAAGGT 59.871 40.000 0.00 0.00 0.00 3.50
2999 3227 5.605534 AGGTGACGATGAATAGATTGAAGG 58.394 41.667 0.00 0.00 0.00 3.46
3000 3228 5.694006 GGAGGTGACGATGAATAGATTGAAG 59.306 44.000 0.00 0.00 0.00 3.02
3001 3229 5.363868 AGGAGGTGACGATGAATAGATTGAA 59.636 40.000 0.00 0.00 0.00 2.69
3002 3230 4.895889 AGGAGGTGACGATGAATAGATTGA 59.104 41.667 0.00 0.00 0.00 2.57
3003 3231 4.987285 CAGGAGGTGACGATGAATAGATTG 59.013 45.833 0.00 0.00 0.00 2.67
3004 3232 4.039730 CCAGGAGGTGACGATGAATAGATT 59.960 45.833 0.00 0.00 0.00 2.40
3005 3233 3.576118 CCAGGAGGTGACGATGAATAGAT 59.424 47.826 0.00 0.00 0.00 1.98
3006 3234 2.959030 CCAGGAGGTGACGATGAATAGA 59.041 50.000 0.00 0.00 0.00 1.98
3007 3235 3.377346 CCAGGAGGTGACGATGAATAG 57.623 52.381 0.00 0.00 0.00 1.73
3015 3243 9.753591 CATAAACTATGAGACCAGGAGGTGACG 62.754 48.148 0.00 0.00 42.92 4.35
3016 3244 6.684111 CATAAACTATGAGACCAGGAGGTGAC 60.684 46.154 0.00 0.00 42.92 3.67
3017 3245 5.363868 CATAAACTATGAGACCAGGAGGTGA 59.636 44.000 0.00 0.00 42.92 4.02
3018 3246 5.129485 ACATAAACTATGAGACCAGGAGGTG 59.871 44.000 0.00 0.00 43.11 4.00
3019 3247 5.281314 ACATAAACTATGAGACCAGGAGGT 58.719 41.667 0.00 0.00 44.54 3.85
3020 3248 5.878406 ACATAAACTATGAGACCAGGAGG 57.122 43.478 0.00 0.00 39.45 4.30
3021 3249 8.183104 TCATACATAAACTATGAGACCAGGAG 57.817 38.462 0.00 0.00 39.45 3.69
3022 3250 7.255977 GCTCATACATAAACTATGAGACCAGGA 60.256 40.741 16.25 0.00 45.78 3.86
3023 3251 6.870965 GCTCATACATAAACTATGAGACCAGG 59.129 42.308 16.25 0.00 45.78 4.45
3024 3252 7.383572 GTGCTCATACATAAACTATGAGACCAG 59.616 40.741 16.25 0.00 45.78 4.00
3025 3253 7.210174 GTGCTCATACATAAACTATGAGACCA 58.790 38.462 16.25 5.90 45.78 4.02
3026 3254 6.363626 CGTGCTCATACATAAACTATGAGACC 59.636 42.308 16.25 6.99 45.78 3.85


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

AutoCloner maintained by Alex Coulton.