Multiple sequence alignment - TraesCS5A01G379700

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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 TraesCS5A01G379700 chr5A 100.000 3038 0 0 1 3038 577431393 577434430 0.000000e+00 5611.0
1 TraesCS5A01G379700 chr5A 98.821 1103 13 0 985 2087 577079361 577078259 0.000000e+00 1965.0
2 TraesCS5A01G379700 chr5A 98.821 1103 13 0 985 2087 577268609 577269711 0.000000e+00 1965.0
3 TraesCS5A01G379700 chr5A 95.333 900 33 4 990 1880 576596402 576597301 0.000000e+00 1421.0
4 TraesCS5A01G379700 chr5A 98.942 567 6 0 985 1551 576949504 576950070 0.000000e+00 1014.0
5 TraesCS5A01G379700 chr5A 89.377 546 44 9 2199 2735 576950620 576951160 0.000000e+00 675.0
6 TraesCS5A01G379700 chr5A 89.377 546 44 9 2199 2735 577078262 577077722 0.000000e+00 675.0
7 TraesCS5A01G379700 chr5A 89.194 546 45 9 2199 2735 577269708 577270248 0.000000e+00 669.0
8 TraesCS5A01G379700 chr5A 98.599 357 5 0 1731 2087 576950267 576950623 1.540000e-177 632.0
9 TraesCS5A01G379700 chr5A 94.839 310 16 0 2658 2967 577270247 577270556 4.550000e-133 484.0
10 TraesCS5A01G379700 chr5A 94.516 310 17 0 2658 2967 577077723 577077414 2.120000e-131 479.0
11 TraesCS5A01G379700 chr5A 94.194 310 18 0 2658 2967 576951159 576951468 9.860000e-130 473.0
12 TraesCS5A01G379700 chr5A 92.857 308 22 0 2660 2967 576612590 576612897 5.970000e-122 448.0
13 TraesCS5A01G379700 chr5A 78.308 650 119 17 1042 1683 687655407 687656042 1.700000e-107 399.0
14 TraesCS5A01G379700 chr5A 87.879 330 36 3 2305 2630 576611266 576611595 4.750000e-103 385.0
15 TraesCS5A01G379700 chr5A 98.450 129 2 0 1959 2087 576610966 576611094 8.470000e-56 228.0
16 TraesCS5A01G379700 chr5A 93.578 109 7 0 1878 1986 576601917 576602025 2.420000e-36 163.0
17 TraesCS5A01G379700 chr5A 86.719 128 17 0 2075 2202 285286050 285286177 3.160000e-30 143.0
18 TraesCS5A01G379700 chr5A 94.444 90 4 1 1878 1967 576602283 576602371 1.470000e-28 137.0
19 TraesCS5A01G379700 chr5A 86.047 129 15 3 2077 2203 340626371 340626244 5.280000e-28 135.0
20 TraesCS5A01G379700 chr5A 89.011 91 9 1 903 992 692556508 692556598 8.900000e-21 111.0
21 TraesCS5A01G379700 chr5D 94.000 1050 58 4 1044 2089 458643562 458644610 0.000000e+00 1585.0
22 TraesCS5A01G379700 chr5D 83.491 424 59 3 2555 2967 458645193 458645616 4.750000e-103 385.0
23 TraesCS5A01G379700 chr5D 88.421 95 9 2 896 990 548858895 548858987 2.480000e-21 113.0
24 TraesCS5A01G379700 chr5B 93.883 1030 63 0 1035 2064 562118774 562119803 0.000000e+00 1554.0
25 TraesCS5A01G379700 chr5B 87.342 158 17 3 2199 2353 562119888 562120045 8.660000e-41 178.0
26 TraesCS5A01G379700 chr5B 92.045 88 7 0 897 984 59694305 59694218 1.140000e-24 124.0
27 TraesCS5A01G379700 chr6B 95.208 626 26 3 366 988 701068200 701068824 0.000000e+00 987.0
28 TraesCS5A01G379700 chr6B 96.800 375 11 1 1 375 701067413 701067786 2.570000e-175 625.0
29 TraesCS5A01G379700 chr6B 94.194 155 9 0 834 988 701070465 701070619 1.410000e-58 237.0
30 TraesCS5A01G379700 chr1D 82.480 976 148 19 1058 2017 442910545 442909577 0.000000e+00 833.0
31 TraesCS5A01G379700 chr4B 79.821 560 89 19 1052 1602 648243504 648244048 1.320000e-103 387.0
32 TraesCS5A01G379700 chr1A 82.712 295 33 11 325 607 43393352 43393064 2.340000e-61 246.0
33 TraesCS5A01G379700 chr1A 95.763 118 5 0 2086 2203 1161219 1161336 1.110000e-44 191.0
34 TraesCS5A01G379700 chr1A 94.915 118 6 0 2085 2202 373262752 373262635 5.170000e-43 185.0
35 TraesCS5A01G379700 chr7D 73.351 773 155 38 1175 1915 24118490 24117737 3.910000e-59 239.0
36 TraesCS5A01G379700 chr7D 93.443 122 7 1 2083 2203 277741953 277741832 2.410000e-41 180.0
37 TraesCS5A01G379700 chr4A 74.428 481 99 18 1175 1643 706089472 706089004 5.170000e-43 185.0
38 TraesCS5A01G379700 chr2D 93.388 121 6 2 2083 2202 400383756 400383637 8.660000e-41 178.0
39 TraesCS5A01G379700 chr3B 89.231 130 12 2 2075 2203 526689426 526689554 8.720000e-36 161.0
40 TraesCS5A01G379700 chr3B 88.542 96 9 2 897 991 818339339 818339245 6.880000e-22 115.0
41 TraesCS5A01G379700 chr6D 87.603 121 13 2 2083 2202 108860646 108860765 4.080000e-29 139.0
42 TraesCS5A01G379700 chr2B 87.395 119 15 0 2085 2203 631261399 631261281 1.470000e-28 137.0
43 TraesCS5A01G379700 chr7B 87.500 96 7 5 890 984 463538334 463538425 4.140000e-19 106.0
44 TraesCS5A01G379700 chr3A 74.793 242 57 4 2689 2927 42108290 42108530 4.140000e-19 106.0
45 TraesCS5A01G379700 chr2A 84.404 109 11 5 896 998 761172055 761171947 5.360000e-18 102.0
46 TraesCS5A01G379700 chr3D 85.000 100 8 5 885 981 519883406 519883311 8.970000e-16 95.3


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 TraesCS5A01G379700 chr5A 577431393 577434430 3037 False 5611.000000 5611 100.000000 1 3038 1 chr5A.!!$F3 3037
1 TraesCS5A01G379700 chr5A 576596402 576597301 899 False 1421.000000 1421 95.333000 990 1880 1 chr5A.!!$F2 890
2 TraesCS5A01G379700 chr5A 577077414 577079361 1947 True 1039.666667 1965 94.238000 985 2967 3 chr5A.!!$R2 1982
3 TraesCS5A01G379700 chr5A 577268609 577270556 1947 False 1039.333333 1965 94.284667 985 2967 3 chr5A.!!$F9 1982
4 TraesCS5A01G379700 chr5A 576949504 576951468 1964 False 698.500000 1014 95.278000 985 2967 4 chr5A.!!$F8 1982
5 TraesCS5A01G379700 chr5A 687655407 687656042 635 False 399.000000 399 78.308000 1042 1683 1 chr5A.!!$F4 641
6 TraesCS5A01G379700 chr5A 576610966 576612897 1931 False 353.666667 448 93.062000 1959 2967 3 chr5A.!!$F7 1008
7 TraesCS5A01G379700 chr5D 458643562 458645616 2054 False 985.000000 1585 88.745500 1044 2967 2 chr5D.!!$F2 1923
8 TraesCS5A01G379700 chr5B 562118774 562120045 1271 False 866.000000 1554 90.612500 1035 2353 2 chr5B.!!$F1 1318
9 TraesCS5A01G379700 chr6B 701067413 701070619 3206 False 616.333333 987 95.400667 1 988 3 chr6B.!!$F1 987
10 TraesCS5A01G379700 chr1D 442909577 442910545 968 True 833.000000 833 82.480000 1058 2017 1 chr1D.!!$R1 959
11 TraesCS5A01G379700 chr4B 648243504 648244048 544 False 387.000000 387 79.821000 1052 1602 1 chr4B.!!$F1 550
12 TraesCS5A01G379700 chr7D 24117737 24118490 753 True 239.000000 239 73.351000 1175 1915 1 chr7D.!!$R1 740

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
824 1251 0.179045 GACCCGGTCCGCTACTAGTA 60.179 60.0 5.5 1.89 0.0 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2189 2733 0.105039 CATCAAGTACTCCCTCCGCC 59.895 60.0 0.0 0.0 0.0 6.13 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
58 59 4.243007 ACTCCTATTGCTGCAACAAAAC 57.757 40.909 18.51 0.00 32.27 2.43
74 75 6.682441 GCAACAAAACAAAGTTGATTTAGTGC 59.318 34.615 9.25 13.28 46.01 4.40
100 101 7.591426 CAGACTGTTAGCAAAGTTGATTTTACC 59.409 37.037 0.00 0.00 0.00 2.85
130 131 5.812642 ACAAGTAATCGGAATGCTCACTAAG 59.187 40.000 0.00 0.00 0.00 2.18
234 235 5.645497 ACAGCATGGATCTAGACTGAAAAAC 59.355 40.000 15.33 0.00 43.62 2.43
327 328 5.125739 CCCCTAACACTAAAACACACAAACA 59.874 40.000 0.00 0.00 0.00 2.83
329 330 7.091443 CCCTAACACTAAAACACACAAACAAA 58.909 34.615 0.00 0.00 0.00 2.83
524 948 2.417719 AGAGTCGATTGAGGCACAAAC 58.582 47.619 0.50 0.00 42.03 2.93
537 961 3.266772 AGGCACAAACCCTAGATTGATGA 59.733 43.478 9.08 0.00 0.00 2.92
716 1142 2.046700 GGGAACGGGCGACATGAA 60.047 61.111 0.00 0.00 0.00 2.57
759 1186 0.401738 CCCCTCTCTCCAAAACTGCA 59.598 55.000 0.00 0.00 0.00 4.41
771 1198 1.722034 AAACTGCAGTCAGAGGGAGA 58.278 50.000 21.95 0.00 42.95 3.71
779 1206 1.283321 AGTCAGAGGGAGAAAATGGGC 59.717 52.381 0.00 0.00 0.00 5.36
821 1248 2.514592 CGACCCGGTCCGCTACTA 60.515 66.667 12.16 0.00 0.00 1.82
822 1249 2.541120 CGACCCGGTCCGCTACTAG 61.541 68.421 12.16 0.00 0.00 2.57
823 1250 1.452833 GACCCGGTCCGCTACTAGT 60.453 63.158 5.50 0.00 0.00 2.57
824 1251 0.179045 GACCCGGTCCGCTACTAGTA 60.179 60.000 5.50 1.89 0.00 1.82
825 1252 0.475906 ACCCGGTCCGCTACTAGTAT 59.524 55.000 5.50 0.00 0.00 2.12
826 1253 1.163554 CCCGGTCCGCTACTAGTATC 58.836 60.000 5.50 0.00 0.00 2.24
827 1254 0.795085 CCGGTCCGCTACTAGTATCG 59.205 60.000 17.15 17.15 0.00 2.92
828 1255 1.606480 CCGGTCCGCTACTAGTATCGA 60.606 57.143 23.85 10.01 0.00 3.59
829 1256 1.458827 CGGTCCGCTACTAGTATCGAC 59.541 57.143 23.85 18.57 0.00 4.20
839 1266 5.972382 GCTACTAGTATCGACCTGAAAACAG 59.028 44.000 2.33 0.00 0.00 3.16
845 1272 2.966309 GACCTGAAAACAGGCCGCG 61.966 63.158 15.02 0.00 46.05 6.46
861 1288 2.661537 CGCGACAGACAACAGCCA 60.662 61.111 0.00 0.00 0.00 4.75
920 1347 4.627900 TGCGCGAATCTTAAAGACATACAA 59.372 37.500 12.10 0.00 0.00 2.41
924 1351 7.621991 CGCGAATCTTAAAGACATACAAGATT 58.378 34.615 0.00 7.85 45.66 2.40
935 1362 5.821470 AGACATACAAGATTCAATGGCTCTG 59.179 40.000 0.00 0.00 32.05 3.35
947 1374 5.181009 TCAATGGCTCTGAACTTAGATGTG 58.819 41.667 0.00 0.00 0.00 3.21
963 1390 8.079203 ACTTAGATGTGAGATAGCTATTTCACG 58.921 37.037 34.39 26.13 45.54 4.35
968 1395 6.960468 TGTGAGATAGCTATTTCACGTCTAG 58.040 40.000 34.39 0.00 45.54 2.43
1270 1711 1.888436 CTTCAGCACCTACTCCGGCA 61.888 60.000 0.00 0.00 0.00 5.69
1758 2231 1.211457 GGGATCAGTGCTGAGTGGAAT 59.789 52.381 7.96 0.00 43.61 3.01
2087 2631 4.952460 TGTTTCTGGAGGTTGTGTAGTAC 58.048 43.478 0.00 0.00 0.00 2.73
2088 2632 4.652421 TGTTTCTGGAGGTTGTGTAGTACT 59.348 41.667 0.00 0.00 0.00 2.73
2089 2633 5.221382 TGTTTCTGGAGGTTGTGTAGTACTC 60.221 44.000 0.00 0.00 0.00 2.59
2090 2634 3.428532 TCTGGAGGTTGTGTAGTACTCC 58.571 50.000 0.00 0.00 46.14 3.85
2091 2635 2.496470 CTGGAGGTTGTGTAGTACTCCC 59.504 54.545 0.00 0.00 45.53 4.30
2092 2636 2.111255 TGGAGGTTGTGTAGTACTCCCT 59.889 50.000 0.00 1.23 45.53 4.20
2093 2637 3.171528 GGAGGTTGTGTAGTACTCCCTT 58.828 50.000 0.00 0.00 41.41 3.95
2094 2638 3.195182 GGAGGTTGTGTAGTACTCCCTTC 59.805 52.174 0.00 0.00 41.41 3.46
2095 2639 2.824341 AGGTTGTGTAGTACTCCCTTCG 59.176 50.000 0.00 0.00 29.39 3.79
2096 2640 2.560105 GGTTGTGTAGTACTCCCTTCGT 59.440 50.000 0.00 0.00 0.00 3.85
2097 2641 3.366781 GGTTGTGTAGTACTCCCTTCGTC 60.367 52.174 0.00 0.00 0.00 4.20
2098 2642 2.440409 TGTGTAGTACTCCCTTCGTCC 58.560 52.381 0.00 0.00 0.00 4.79
2099 2643 1.399791 GTGTAGTACTCCCTTCGTCCG 59.600 57.143 0.00 0.00 0.00 4.79
2100 2644 1.020437 GTAGTACTCCCTTCGTCCGG 58.980 60.000 0.00 0.00 0.00 5.14
2101 2645 0.911769 TAGTACTCCCTTCGTCCGGA 59.088 55.000 0.00 0.00 0.00 5.14
2102 2646 0.038744 AGTACTCCCTTCGTCCGGAA 59.961 55.000 5.23 0.00 0.00 4.30
2103 2647 0.890683 GTACTCCCTTCGTCCGGAAA 59.109 55.000 5.23 0.00 33.34 3.13
2104 2648 1.479730 GTACTCCCTTCGTCCGGAAAT 59.520 52.381 5.23 0.00 33.34 2.17
2105 2649 1.856629 ACTCCCTTCGTCCGGAAATA 58.143 50.000 5.23 0.00 33.34 1.40
2106 2650 1.479730 ACTCCCTTCGTCCGGAAATAC 59.520 52.381 5.23 0.00 33.34 1.89
2107 2651 1.755380 CTCCCTTCGTCCGGAAATACT 59.245 52.381 5.23 0.00 33.34 2.12
2108 2652 2.167900 CTCCCTTCGTCCGGAAATACTT 59.832 50.000 5.23 0.00 33.34 2.24
2109 2653 2.093869 TCCCTTCGTCCGGAAATACTTG 60.094 50.000 5.23 0.00 33.34 3.16
2110 2654 2.354403 CCCTTCGTCCGGAAATACTTGT 60.354 50.000 5.23 0.00 33.34 3.16
2111 2655 2.928116 CCTTCGTCCGGAAATACTTGTC 59.072 50.000 5.23 0.00 33.34 3.18
2112 2656 2.660189 TCGTCCGGAAATACTTGTCC 57.340 50.000 5.23 0.00 0.00 4.02
2113 2657 1.205417 TCGTCCGGAAATACTTGTCCC 59.795 52.381 5.23 0.00 0.00 4.46
2114 2658 1.066716 CGTCCGGAAATACTTGTCCCA 60.067 52.381 5.23 0.00 0.00 4.37
2115 2659 2.613474 CGTCCGGAAATACTTGTCCCAA 60.613 50.000 5.23 0.00 0.00 4.12
2116 2660 3.414269 GTCCGGAAATACTTGTCCCAAA 58.586 45.455 5.23 0.00 0.00 3.28
2117 2661 3.822167 GTCCGGAAATACTTGTCCCAAAA 59.178 43.478 5.23 0.00 0.00 2.44
2118 2662 4.278919 GTCCGGAAATACTTGTCCCAAAAA 59.721 41.667 5.23 0.00 0.00 1.94
2119 2663 5.047590 GTCCGGAAATACTTGTCCCAAAAAT 60.048 40.000 5.23 0.00 0.00 1.82
2120 2664 6.151480 GTCCGGAAATACTTGTCCCAAAAATA 59.849 38.462 5.23 0.00 0.00 1.40
2121 2665 6.376018 TCCGGAAATACTTGTCCCAAAAATAG 59.624 38.462 0.00 0.00 0.00 1.73
2122 2666 6.376018 CCGGAAATACTTGTCCCAAAAATAGA 59.624 38.462 0.00 0.00 0.00 1.98
2123 2667 7.068226 CCGGAAATACTTGTCCCAAAAATAGAT 59.932 37.037 0.00 0.00 0.00 1.98
2124 2668 7.915397 CGGAAATACTTGTCCCAAAAATAGATG 59.085 37.037 0.00 0.00 0.00 2.90
2125 2669 8.749354 GGAAATACTTGTCCCAAAAATAGATGT 58.251 33.333 0.00 0.00 0.00 3.06
2131 2675 9.838339 ACTTGTCCCAAAAATAGATGTATCTAG 57.162 33.333 7.57 0.00 42.20 2.43
2133 2677 9.832445 TTGTCCCAAAAATAGATGTATCTAGAC 57.168 33.333 0.00 7.60 42.20 2.59
2134 2678 8.141909 TGTCCCAAAAATAGATGTATCTAGACG 58.858 37.037 0.00 0.00 42.20 4.18
2135 2679 8.142551 GTCCCAAAAATAGATGTATCTAGACGT 58.857 37.037 0.00 0.00 42.20 4.34
2136 2680 9.358406 TCCCAAAAATAGATGTATCTAGACGTA 57.642 33.333 0.00 0.00 42.20 3.57
2176 2720 6.978343 ATCCGTTTCTATTCATTTTCGTGA 57.022 33.333 0.00 0.00 0.00 4.35
2177 2721 6.160664 TCCGTTTCTATTCATTTTCGTGAC 57.839 37.500 0.00 0.00 0.00 3.67
2178 2722 5.697178 TCCGTTTCTATTCATTTTCGTGACA 59.303 36.000 0.00 0.00 0.00 3.58
2179 2723 6.203145 TCCGTTTCTATTCATTTTCGTGACAA 59.797 34.615 0.00 0.00 0.00 3.18
2180 2724 6.519761 CCGTTTCTATTCATTTTCGTGACAAG 59.480 38.462 0.00 0.00 0.00 3.16
2181 2725 7.069569 CGTTTCTATTCATTTTCGTGACAAGT 58.930 34.615 0.00 0.00 0.00 3.16
2182 2726 8.218441 CGTTTCTATTCATTTTCGTGACAAGTA 58.782 33.333 0.00 0.00 0.00 2.24
2183 2727 9.872757 GTTTCTATTCATTTTCGTGACAAGTAA 57.127 29.630 0.00 0.00 0.00 2.24
2189 2733 7.372451 TCATTTTCGTGACAAGTAATTAGGG 57.628 36.000 0.00 0.00 0.00 3.53
2190 2734 6.373216 TCATTTTCGTGACAAGTAATTAGGGG 59.627 38.462 0.00 0.00 0.00 4.79
2191 2735 3.255969 TCGTGACAAGTAATTAGGGGC 57.744 47.619 0.00 0.00 0.00 5.80
2192 2736 1.931172 CGTGACAAGTAATTAGGGGCG 59.069 52.381 0.00 0.00 0.00 6.13
2193 2737 2.285977 GTGACAAGTAATTAGGGGCGG 58.714 52.381 0.00 0.00 0.00 6.13
2194 2738 2.093341 GTGACAAGTAATTAGGGGCGGA 60.093 50.000 0.00 0.00 0.00 5.54
2195 2739 2.169769 TGACAAGTAATTAGGGGCGGAG 59.830 50.000 0.00 0.00 0.00 4.63
2196 2740 1.489230 ACAAGTAATTAGGGGCGGAGG 59.511 52.381 0.00 0.00 0.00 4.30
2197 2741 1.137697 AAGTAATTAGGGGCGGAGGG 58.862 55.000 0.00 0.00 0.00 4.30
2198 2742 0.266753 AGTAATTAGGGGCGGAGGGA 59.733 55.000 0.00 0.00 0.00 4.20
2254 2798 3.253188 GCAGCAACCACTAAACATGAAGA 59.747 43.478 0.00 0.00 0.00 2.87
2264 2815 8.867097 ACCACTAAACATGAAGAGTAGACTTAA 58.133 33.333 0.00 0.00 0.00 1.85
2265 2816 9.877178 CCACTAAACATGAAGAGTAGACTTAAT 57.123 33.333 0.00 0.00 0.00 1.40
2343 2966 0.509929 CATGGCTATGTGCATCGACG 59.490 55.000 1.12 0.00 45.15 5.12
2409 3032 8.396272 GGCTTTGCCTTATCTATTAATCAAGA 57.604 34.615 0.73 0.00 46.69 3.02
2414 3037 8.839310 TGCCTTATCTATTAATCAAGAAGAGC 57.161 34.615 0.00 2.16 0.00 4.09
2429 3052 8.902540 TCAAGAAGAGCATAGAGTTTTACAAA 57.097 30.769 0.00 0.00 0.00 2.83
2434 3057 8.854614 AAGAGCATAGAGTTTTACAAATGTCT 57.145 30.769 0.00 0.00 0.00 3.41
2476 3099 5.591643 ATTACTCGCGCAATATAACTTGG 57.408 39.130 8.75 0.00 0.00 3.61
2482 3105 3.399330 GCGCAATATAACTTGGCCTAGA 58.601 45.455 21.63 0.00 0.00 2.43
2489 3113 9.284968 GCAATATAACTTGGCCTAGATTTTAGA 57.715 33.333 21.63 6.99 0.00 2.10
2495 3119 2.219458 GGCCTAGATTTTAGAACCCGC 58.781 52.381 0.00 0.00 0.00 6.13
2502 3126 0.393820 TTTTAGAACCCGCGGTGACT 59.606 50.000 26.12 20.46 35.34 3.41
2534 3158 4.092529 CACCTCGTCAAAGATGATGTTCAG 59.907 45.833 0.00 0.00 42.22 3.02
2541 3165 6.256686 GTCAAAGATGATGTTCAGCAAGATC 58.743 40.000 0.00 0.00 34.77 2.75
2548 3174 0.955428 GTTCAGCAAGATCGGTGGCA 60.955 55.000 2.20 0.00 35.11 4.92
2559 3677 2.521708 GGTGGCAGGGCACACTTT 60.522 61.111 24.55 0.00 37.72 2.66
2572 3690 1.063469 CACACTTTTGCCGAAAGACGT 59.937 47.619 11.41 5.16 46.24 4.34
2578 3696 2.228138 TTGCCGAAAGACGTGTAAGT 57.772 45.000 0.00 0.00 40.78 2.24
2585 3703 4.382160 CCGAAAGACGTGTAAGTTTCTCTC 59.618 45.833 0.00 0.00 40.78 3.20
2610 3732 6.402550 CGTCCATATTTTCCAAGAGACAAGTG 60.403 42.308 0.00 0.00 0.00 3.16
2639 4650 0.247736 AGGTCATGGCTCGACTGTTC 59.752 55.000 0.00 0.00 33.73 3.18
2652 4663 0.673437 ACTGTTCGGGTTTTGCATGG 59.327 50.000 0.00 0.00 0.00 3.66
2678 4689 3.526899 TCTCTTGTCCCACCAATCCTTA 58.473 45.455 0.00 0.00 0.00 2.69
2740 4903 2.008242 AGGCCTAGCTTCTCGATGAT 57.992 50.000 1.29 0.00 0.00 2.45
2791 4954 4.100653 CACTTGAAGGATAGATGAGCTCCA 59.899 45.833 12.15 0.00 0.00 3.86
2792 4955 4.718774 ACTTGAAGGATAGATGAGCTCCAA 59.281 41.667 12.15 3.03 0.00 3.53
2970 5142 3.200522 GCCAAGGAATTGAGGCGG 58.799 61.111 0.00 0.00 37.41 6.13
2971 5143 1.678970 GCCAAGGAATTGAGGCGGT 60.679 57.895 0.00 0.00 37.41 5.68
2972 5144 1.937546 GCCAAGGAATTGAGGCGGTG 61.938 60.000 0.00 0.00 37.41 4.94
2973 5145 1.315257 CCAAGGAATTGAGGCGGTGG 61.315 60.000 0.00 0.00 0.00 4.61
2974 5146 0.322456 CAAGGAATTGAGGCGGTGGA 60.322 55.000 0.00 0.00 0.00 4.02
2975 5147 0.322546 AAGGAATTGAGGCGGTGGAC 60.323 55.000 0.00 0.00 0.00 4.02
2987 5159 2.674296 GGTGGACGCCGAATAGAAC 58.326 57.895 0.00 0.00 0.00 3.01
2988 5160 0.808847 GGTGGACGCCGAATAGAACC 60.809 60.000 0.00 0.00 0.00 3.62
2991 5163 2.033372 TGGACGCCGAATAGAACCATA 58.967 47.619 0.00 0.00 0.00 2.74
2992 5164 2.631062 TGGACGCCGAATAGAACCATAT 59.369 45.455 0.00 0.00 0.00 1.78
2993 5165 2.993899 GGACGCCGAATAGAACCATATG 59.006 50.000 0.00 0.00 0.00 1.78
2994 5166 3.554337 GGACGCCGAATAGAACCATATGT 60.554 47.826 1.24 0.00 0.00 2.29
2995 5167 3.650139 ACGCCGAATAGAACCATATGTC 58.350 45.455 1.24 0.00 0.00 3.06
2996 5168 3.069016 ACGCCGAATAGAACCATATGTCA 59.931 43.478 1.24 0.00 0.00 3.58
2997 5169 4.245660 CGCCGAATAGAACCATATGTCAT 58.754 43.478 1.24 0.00 0.00 3.06
2998 5170 4.690748 CGCCGAATAGAACCATATGTCATT 59.309 41.667 1.24 0.00 0.00 2.57
3000 5172 6.293407 CGCCGAATAGAACCATATGTCATTTT 60.293 38.462 1.24 0.00 0.00 1.82
3001 5173 7.425606 GCCGAATAGAACCATATGTCATTTTT 58.574 34.615 1.24 0.00 0.00 1.94
3022 5194 3.774282 TTCAAAATACGACACGTTCCG 57.226 42.857 1.53 4.97 41.54 4.30
3023 5195 1.456544 TCAAAATACGACACGTTCCGC 59.543 47.619 1.53 0.00 41.54 5.54
3024 5196 1.192757 CAAAATACGACACGTTCCGCA 59.807 47.619 1.53 0.00 41.54 5.69
3025 5197 1.717194 AAATACGACACGTTCCGCAT 58.283 45.000 1.53 0.00 41.54 4.73
3028 5200 0.039346 TACGACACGTTCCGCATCAA 60.039 50.000 1.53 0.00 41.54 2.57
3030 5202 0.442310 CGACACGTTCCGCATCAAAT 59.558 50.000 0.00 0.00 0.00 2.32
3031 5203 1.136085 CGACACGTTCCGCATCAAATT 60.136 47.619 0.00 0.00 0.00 1.82
3032 5204 2.241722 GACACGTTCCGCATCAAATTG 58.758 47.619 0.00 0.00 0.00 2.32
3033 5205 1.068610 ACACGTTCCGCATCAAATTGG 60.069 47.619 0.00 0.00 0.00 3.16
3034 5206 0.109319 ACGTTCCGCATCAAATTGGC 60.109 50.000 0.00 0.00 0.00 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 6.064846 ACAGTCTGCACTAAATCAACTTTG 57.935 37.500 0.00 0.00 0.00 2.77
74 75 7.591426 GGTAAAATCAACTTTGCTAACAGTCTG 59.409 37.037 0.00 0.00 0.00 3.51
100 101 3.063997 GCATTCCGATTACTTGTGTCAGG 59.936 47.826 0.00 0.00 0.00 3.86
130 131 7.367285 TGTACATGTGCCTTTTCTTATTTGTC 58.633 34.615 9.11 0.00 0.00 3.18
144 145 7.228507 TCCAGTATCATAATTTGTACATGTGCC 59.771 37.037 9.11 0.00 0.00 5.01
213 214 6.500684 TTGTTTTTCAGTCTAGATCCATGC 57.499 37.500 0.00 0.00 0.00 4.06
283 284 5.479027 AGGGGTTTAAACGATATGCAGTTTT 59.521 36.000 12.07 0.00 40.54 2.43
284 285 5.014202 AGGGGTTTAAACGATATGCAGTTT 58.986 37.500 12.07 6.96 42.43 2.66
329 330 7.286087 TGCAGAGATTCAGTATATGCCATTTTT 59.714 33.333 0.00 0.00 0.00 1.94
420 844 6.555463 ATCTAAGGTTCGTTCCCTCAAATA 57.445 37.500 0.00 0.00 0.00 1.40
524 948 7.864108 TTGTTTGTGTATCATCAATCTAGGG 57.136 36.000 0.00 0.00 0.00 3.53
537 961 7.255942 CCATCCCTCTTCTTTTTGTTTGTGTAT 60.256 37.037 0.00 0.00 0.00 2.29
582 1006 5.622770 ATTGTTTCTGTCCGGTTATTGTC 57.377 39.130 0.00 0.00 0.00 3.18
681 1107 0.462759 CCCATTCCTCTTCGACAGGC 60.463 60.000 4.88 0.00 0.00 4.85
686 1112 0.535335 CGTTCCCCATTCCTCTTCGA 59.465 55.000 0.00 0.00 0.00 3.71
691 1117 2.124278 GCCCGTTCCCCATTCCTC 60.124 66.667 0.00 0.00 0.00 3.71
716 1142 1.693404 CCATCCATTTTCCCCTGGCAT 60.693 52.381 0.00 0.00 32.30 4.40
759 1186 1.283321 GCCCATTTTCTCCCTCTGACT 59.717 52.381 0.00 0.00 0.00 3.41
779 1206 1.817941 CGATAGTTGGGTTGGGCGG 60.818 63.158 0.00 0.00 0.00 6.13
786 1213 0.734942 CGTTGTCGCGATAGTTGGGT 60.735 55.000 14.06 0.00 39.35 4.51
812 1239 2.366590 TCAGGTCGATACTAGTAGCGGA 59.633 50.000 32.99 22.08 44.12 5.54
845 1272 2.939022 GTGGCTGTTGTCTGTCGC 59.061 61.111 0.00 0.00 0.00 5.19
899 1326 6.569228 TCTTGTATGTCTTTAAGATTCGCG 57.431 37.500 0.00 0.00 0.00 5.87
920 1347 6.305272 TCTAAGTTCAGAGCCATTGAATCT 57.695 37.500 0.00 0.00 36.96 2.40
924 1351 5.046376 TCACATCTAAGTTCAGAGCCATTGA 60.046 40.000 0.00 0.00 0.00 2.57
935 1362 9.973450 TGAAATAGCTATCTCACATCTAAGTTC 57.027 33.333 5.61 2.90 0.00 3.01
947 1374 7.748683 CACATCTAGACGTGAAATAGCTATCTC 59.251 40.741 13.63 2.99 35.02 2.75
963 1390 6.701841 TCGGATTTGCTATTTCACATCTAGAC 59.298 38.462 0.00 0.00 0.00 2.59
968 1395 6.638468 GGAAATCGGATTTGCTATTTCACATC 59.362 38.462 22.78 5.06 39.16 3.06
1013 1440 8.709308 AGGAGAACATTTTACATAGTAGCTCAT 58.291 33.333 0.00 0.00 0.00 2.90
1623 2073 3.356639 GAGCCGCGTGGTGATCTCA 62.357 63.158 17.91 0.00 37.67 3.27
1758 2231 1.043816 GGATCGCCCAGAAGAGATCA 58.956 55.000 7.42 0.00 40.74 2.92
1934 2407 4.148825 CGGCCACCTCTTCTCCCG 62.149 72.222 2.24 0.00 0.00 5.14
2087 2631 1.755380 AGTATTTCCGGACGAAGGGAG 59.245 52.381 1.83 0.00 33.01 4.30
2088 2632 1.856629 AGTATTTCCGGACGAAGGGA 58.143 50.000 1.83 0.00 0.00 4.20
2089 2633 2.277084 CAAGTATTTCCGGACGAAGGG 58.723 52.381 1.83 0.00 0.00 3.95
2090 2634 2.928116 GACAAGTATTTCCGGACGAAGG 59.072 50.000 1.83 0.00 0.00 3.46
2091 2635 2.928116 GGACAAGTATTTCCGGACGAAG 59.072 50.000 1.83 0.00 0.00 3.79
2092 2636 2.354003 GGGACAAGTATTTCCGGACGAA 60.354 50.000 1.83 0.00 32.00 3.85
2093 2637 1.205417 GGGACAAGTATTTCCGGACGA 59.795 52.381 1.83 0.00 32.00 4.20
2094 2638 1.066716 TGGGACAAGTATTTCCGGACG 60.067 52.381 1.83 0.00 31.92 4.79
2095 2639 2.773993 TGGGACAAGTATTTCCGGAC 57.226 50.000 1.83 0.00 31.92 4.79
2105 2649 9.838339 CTAGATACATCTATTTTTGGGACAAGT 57.162 33.333 0.00 0.00 40.37 3.16
2107 2651 9.832445 GTCTAGATACATCTATTTTTGGGACAA 57.168 33.333 0.00 0.00 40.37 3.18
2108 2652 8.141909 CGTCTAGATACATCTATTTTTGGGACA 58.858 37.037 0.00 0.00 38.60 4.02
2109 2653 8.142551 ACGTCTAGATACATCTATTTTTGGGAC 58.857 37.037 0.00 2.21 38.60 4.46
2110 2654 8.246430 ACGTCTAGATACATCTATTTTTGGGA 57.754 34.615 0.00 0.00 38.60 4.37
2150 2694 9.752961 TCACGAAAATGAATAGAAACGGATATA 57.247 29.630 0.00 0.00 0.00 0.86
2151 2695 8.548721 GTCACGAAAATGAATAGAAACGGATAT 58.451 33.333 0.00 0.00 0.00 1.63
2152 2696 7.546316 TGTCACGAAAATGAATAGAAACGGATA 59.454 33.333 0.00 0.00 0.00 2.59
2153 2697 6.370442 TGTCACGAAAATGAATAGAAACGGAT 59.630 34.615 0.00 0.00 0.00 4.18
2154 2698 5.697178 TGTCACGAAAATGAATAGAAACGGA 59.303 36.000 0.00 0.00 0.00 4.69
2155 2699 5.922546 TGTCACGAAAATGAATAGAAACGG 58.077 37.500 0.00 0.00 0.00 4.44
2156 2700 7.069569 ACTTGTCACGAAAATGAATAGAAACG 58.930 34.615 0.00 0.00 0.00 3.60
2157 2701 9.872757 TTACTTGTCACGAAAATGAATAGAAAC 57.127 29.630 0.00 0.00 0.00 2.78
2163 2707 8.458843 CCCTAATTACTTGTCACGAAAATGAAT 58.541 33.333 0.00 0.00 0.00 2.57
2164 2708 7.094549 CCCCTAATTACTTGTCACGAAAATGAA 60.095 37.037 0.00 0.00 0.00 2.57
2165 2709 6.373216 CCCCTAATTACTTGTCACGAAAATGA 59.627 38.462 0.00 0.00 0.00 2.57
2166 2710 6.551736 CCCCTAATTACTTGTCACGAAAATG 58.448 40.000 0.00 0.00 0.00 2.32
2167 2711 5.124936 GCCCCTAATTACTTGTCACGAAAAT 59.875 40.000 0.00 0.00 0.00 1.82
2168 2712 4.456566 GCCCCTAATTACTTGTCACGAAAA 59.543 41.667 0.00 0.00 0.00 2.29
2169 2713 4.004982 GCCCCTAATTACTTGTCACGAAA 58.995 43.478 0.00 0.00 0.00 3.46
2170 2714 3.602483 GCCCCTAATTACTTGTCACGAA 58.398 45.455 0.00 0.00 0.00 3.85
2171 2715 2.417651 CGCCCCTAATTACTTGTCACGA 60.418 50.000 0.00 0.00 0.00 4.35
2172 2716 1.931172 CGCCCCTAATTACTTGTCACG 59.069 52.381 0.00 0.00 0.00 4.35
2173 2717 2.093341 TCCGCCCCTAATTACTTGTCAC 60.093 50.000 0.00 0.00 0.00 3.67
2174 2718 2.169769 CTCCGCCCCTAATTACTTGTCA 59.830 50.000 0.00 0.00 0.00 3.58
2175 2719 2.484947 CCTCCGCCCCTAATTACTTGTC 60.485 54.545 0.00 0.00 0.00 3.18
2176 2720 1.489230 CCTCCGCCCCTAATTACTTGT 59.511 52.381 0.00 0.00 0.00 3.16
2177 2721 1.202770 CCCTCCGCCCCTAATTACTTG 60.203 57.143 0.00 0.00 0.00 3.16
2178 2722 1.137697 CCCTCCGCCCCTAATTACTT 58.862 55.000 0.00 0.00 0.00 2.24
2179 2723 0.266753 TCCCTCCGCCCCTAATTACT 59.733 55.000 0.00 0.00 0.00 2.24
2180 2724 0.685660 CTCCCTCCGCCCCTAATTAC 59.314 60.000 0.00 0.00 0.00 1.89
2181 2725 0.266753 ACTCCCTCCGCCCCTAATTA 59.733 55.000 0.00 0.00 0.00 1.40
2182 2726 0.266753 TACTCCCTCCGCCCCTAATT 59.733 55.000 0.00 0.00 0.00 1.40
2183 2727 0.471401 GTACTCCCTCCGCCCCTAAT 60.471 60.000 0.00 0.00 0.00 1.73
2184 2728 1.075748 GTACTCCCTCCGCCCCTAA 60.076 63.158 0.00 0.00 0.00 2.69
2185 2729 1.587522 AAGTACTCCCTCCGCCCCTA 61.588 60.000 0.00 0.00 0.00 3.53
2186 2730 2.944668 AAGTACTCCCTCCGCCCCT 61.945 63.158 0.00 0.00 0.00 4.79
2187 2731 2.365237 AAGTACTCCCTCCGCCCC 60.365 66.667 0.00 0.00 0.00 5.80
2188 2732 1.049289 ATCAAGTACTCCCTCCGCCC 61.049 60.000 0.00 0.00 0.00 6.13
2189 2733 0.105039 CATCAAGTACTCCCTCCGCC 59.895 60.000 0.00 0.00 0.00 6.13
2190 2734 1.112113 TCATCAAGTACTCCCTCCGC 58.888 55.000 0.00 0.00 0.00 5.54
2191 2735 3.226777 AGATCATCAAGTACTCCCTCCG 58.773 50.000 0.00 0.00 0.00 4.63
2192 2736 4.202305 CCAAGATCATCAAGTACTCCCTCC 60.202 50.000 0.00 0.00 0.00 4.30
2193 2737 4.651503 TCCAAGATCATCAAGTACTCCCTC 59.348 45.833 0.00 0.00 0.00 4.30
2194 2738 4.407296 GTCCAAGATCATCAAGTACTCCCT 59.593 45.833 0.00 0.00 0.00 4.20
2195 2739 4.407296 AGTCCAAGATCATCAAGTACTCCC 59.593 45.833 0.00 0.00 0.00 4.30
2196 2740 5.355596 CAGTCCAAGATCATCAAGTACTCC 58.644 45.833 0.00 0.00 0.00 3.85
2197 2741 5.355596 CCAGTCCAAGATCATCAAGTACTC 58.644 45.833 0.00 0.00 0.00 2.59
2198 2742 4.163078 CCCAGTCCAAGATCATCAAGTACT 59.837 45.833 0.00 0.00 0.00 2.73
2264 2815 6.948309 AGGTGAAGTTGGCTGTTTCTTATAAT 59.052 34.615 0.00 0.00 0.00 1.28
2265 2816 6.303839 AGGTGAAGTTGGCTGTTTCTTATAA 58.696 36.000 0.00 0.00 0.00 0.98
2266 2817 5.876357 AGGTGAAGTTGGCTGTTTCTTATA 58.124 37.500 0.00 0.00 0.00 0.98
2267 2818 4.729868 AGGTGAAGTTGGCTGTTTCTTAT 58.270 39.130 0.00 0.00 0.00 1.73
2302 2853 7.970614 CCATGTTAAGTTGGCTCTTTCTTATTC 59.029 37.037 0.00 0.00 0.00 1.75
2409 3032 8.854614 AGACATTTGTAAAACTCTATGCTCTT 57.145 30.769 0.00 0.00 0.00 2.85
2429 3052 8.771920 TCGTCATGTTATGTTTTAAGAGACAT 57.228 30.769 0.00 6.48 39.62 3.06
2472 3095 3.877508 CGGGTTCTAAAATCTAGGCCAAG 59.122 47.826 5.01 0.00 0.00 3.61
2476 3099 1.865340 CGCGGGTTCTAAAATCTAGGC 59.135 52.381 0.00 0.00 0.00 3.93
2482 3105 1.002773 AGTCACCGCGGGTTCTAAAAT 59.997 47.619 31.76 0.57 31.02 1.82
2489 3113 1.255667 ACTATGAGTCACCGCGGGTT 61.256 55.000 31.76 11.64 31.02 4.11
2502 3126 5.462530 TCTTTGACGAGGTGAAACTATGA 57.537 39.130 0.00 0.00 36.74 2.15
2534 3158 2.825836 CCCTGCCACCGATCTTGC 60.826 66.667 0.00 0.00 0.00 4.01
2541 3165 4.954970 AAGTGTGCCCTGCCACCG 62.955 66.667 0.00 0.00 34.85 4.94
2559 3677 2.228138 ACTTACACGTCTTTCGGCAA 57.772 45.000 0.00 0.00 44.69 4.52
2572 3690 7.548075 GGAAAATATGGACGAGAGAAACTTACA 59.452 37.037 0.00 0.00 0.00 2.41
2578 3696 6.707290 TCTTGGAAAATATGGACGAGAGAAA 58.293 36.000 0.00 0.00 0.00 2.52
2585 3703 5.643777 ACTTGTCTCTTGGAAAATATGGACG 59.356 40.000 0.00 0.00 0.00 4.79
2610 3732 0.678048 GCCATGACCTTCCTCACCAC 60.678 60.000 0.00 0.00 0.00 4.16
2639 4650 0.667184 GAACAGCCATGCAAAACCCG 60.667 55.000 0.00 0.00 0.00 5.28
2652 4663 0.108585 TGGTGGGACAAGAGAACAGC 59.891 55.000 0.00 0.00 44.16 4.40
2678 4689 1.250840 GGCATTTGGACGGCTCCTTT 61.251 55.000 0.00 0.00 37.48 3.11
2687 4774 1.895131 ACATCCACTTGGCATTTGGAC 59.105 47.619 17.32 0.00 42.26 4.02
2740 4903 2.716424 ACCCTTGGACTTTGGAGATTGA 59.284 45.455 0.00 0.00 0.00 2.57
2791 4954 7.360113 TCTTTGTAAAAGGGAGCAAGAAATT 57.640 32.000 0.20 0.00 0.00 1.82
2792 4955 6.015095 CCTCTTTGTAAAAGGGAGCAAGAAAT 60.015 38.462 1.10 0.00 0.00 2.17
2915 5078 1.777272 GGATCTCATAGTTTGGGCCCT 59.223 52.381 25.70 4.56 0.00 5.19
2969 5141 0.808847 GGTTCTATTCGGCGTCCACC 60.809 60.000 6.85 2.30 0.00 4.61
2970 5142 0.108520 TGGTTCTATTCGGCGTCCAC 60.109 55.000 6.85 0.00 0.00 4.02
2971 5143 0.828022 ATGGTTCTATTCGGCGTCCA 59.172 50.000 6.85 6.12 0.00 4.02
2972 5144 2.806608 TATGGTTCTATTCGGCGTCC 57.193 50.000 6.85 0.44 0.00 4.79
2973 5145 3.650139 ACATATGGTTCTATTCGGCGTC 58.350 45.455 6.85 0.00 0.00 5.19
2974 5146 3.069016 TGACATATGGTTCTATTCGGCGT 59.931 43.478 6.85 0.00 0.00 5.68
2975 5147 3.649073 TGACATATGGTTCTATTCGGCG 58.351 45.455 7.80 0.00 0.00 6.46
2976 5148 6.560253 AAATGACATATGGTTCTATTCGGC 57.440 37.500 7.80 0.00 0.00 5.54


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

AutoCloner maintained by Alex Coulton.