Multiple sequence alignment - TraesCS2D01G014500

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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 TraesCS2D01G014500 chr2D 100.000 4561 0 0 1 4561 7075799 7071239 0.000000e+00 8423.0
1 TraesCS2D01G014500 chr2D 87.584 2239 227 25 1416 3621 7087502 7085282 0.000000e+00 2547.0
2 TraesCS2D01G014500 chr2D 81.102 1651 240 47 2007 3622 7091649 7090036 0.000000e+00 1254.0
3 TraesCS2D01G014500 chr2D 80.999 1642 222 45 2007 3596 7064771 7066374 0.000000e+00 1221.0
4 TraesCS2D01G014500 chr2D 80.808 1584 224 47 2054 3621 7002193 7003712 0.000000e+00 1168.0
5 TraesCS2D01G014500 chr2D 87.738 367 42 1 1454 1820 7001656 7002019 4.220000e-115 425.0
6 TraesCS2D01G014500 chr2D 79.719 498 67 17 4064 4561 433725840 433725377 3.400000e-86 329.0
7 TraesCS2D01G014500 chr2D 85.069 288 34 8 964 1244 7088050 7087765 7.470000e-73 285.0
8 TraesCS2D01G014500 chr2D 83.333 252 40 2 4300 4551 228538554 228538803 9.870000e-57 231.0
9 TraesCS2D01G014500 chr2D 82.900 269 32 7 940 1197 7093073 7092808 3.550000e-56 230.0
10 TraesCS2D01G014500 chr2D 83.137 255 40 3 279 531 421011757 421012010 3.550000e-56 230.0
11 TraesCS2D01G014500 chr2D 80.702 285 33 12 930 1194 7000522 7000804 7.740000e-48 202.0
12 TraesCS2D01G014500 chr2B 95.645 1952 70 11 1957 3901 2236438 2238381 0.000000e+00 3120.0
13 TraesCS2D01G014500 chr2B 95.532 1947 78 6 1957 3901 2503097 2501158 0.000000e+00 3105.0
14 TraesCS2D01G014500 chr2B 86.711 1806 185 26 1851 3621 2219074 2220859 0.000000e+00 1954.0
15 TraesCS2D01G014500 chr2B 92.152 1236 45 20 645 1838 2235211 2236436 0.000000e+00 1698.0
16 TraesCS2D01G014500 chr2B 87.674 1079 102 17 1851 2916 2512957 2511897 0.000000e+00 1227.0
17 TraesCS2D01G014500 chr2B 80.577 1663 236 50 2007 3607 2346242 2344605 0.000000e+00 1201.0
18 TraesCS2D01G014500 chr2B 91.236 890 38 14 988 1838 2503987 2503099 0.000000e+00 1175.0
19 TraesCS2D01G014500 chr2B 80.408 1618 242 37 2010 3597 2527654 2526082 0.000000e+00 1162.0
20 TraesCS2D01G014500 chr2B 80.891 1392 205 36 2229 3597 2131345 2132698 0.000000e+00 1040.0
21 TraesCS2D01G014500 chr2B 92.612 582 38 2 3903 4484 2250899 2251475 0.000000e+00 832.0
22 TraesCS2D01G014500 chr2B 85.859 792 61 28 169 912 2504781 2503993 0.000000e+00 795.0
23 TraesCS2D01G014500 chr2B 88.216 611 60 6 3021 3621 2511816 2511208 0.000000e+00 719.0
24 TraesCS2D01G014500 chr2B 88.512 383 43 1 1416 1797 2218375 2218757 3.210000e-126 462.0
25 TraesCS2D01G014500 chr2B 76.663 917 144 35 2706 3596 2269885 2269013 1.160000e-120 444.0
26 TraesCS2D01G014500 chr2B 89.736 341 35 0 1457 1797 2346923 2346583 1.950000e-118 436.0
27 TraesCS2D01G014500 chr2B 92.233 206 9 2 1 200 2234421 2234625 7.470000e-73 285.0
28 TraesCS2D01G014500 chr2B 84.921 252 24 6 1 240 2505014 2504765 4.560000e-60 243.0
29 TraesCS2D01G014500 chr2B 87.215 219 19 8 964 1175 2136126 2136342 1.640000e-59 241.0
30 TraesCS2D01G014500 chr2B 78.218 404 59 17 819 1197 2348049 2347650 9.870000e-57 231.0
31 TraesCS2D01G014500 chr2B 85.222 203 26 4 4062 4263 694324542 694324741 5.980000e-49 206.0
32 TraesCS2D01G014500 chr2B 87.879 165 15 5 978 1139 2523635 2523473 6.020000e-44 189.0
33 TraesCS2D01G014500 chr2B 87.975 158 18 1 1088 1244 2523236 2523079 7.790000e-43 185.0
34 TraesCS2D01G014500 chr2A 86.908 2513 258 32 1416 3891 5485501 5483023 0.000000e+00 2752.0
35 TraesCS2D01G014500 chr2A 80.804 1641 217 56 2007 3607 5310413 5311995 0.000000e+00 1195.0
36 TraesCS2D01G014500 chr2A 80.974 1561 230 39 2091 3622 5527648 5526126 0.000000e+00 1175.0
37 TraesCS2D01G014500 chr2A 90.164 366 33 1 1454 1819 5189279 5189641 1.490000e-129 473.0
38 TraesCS2D01G014500 chr2A 90.029 341 33 1 1457 1796 5528353 5528013 1.510000e-119 440.0
39 TraesCS2D01G014500 chr2A 88.043 368 39 4 1435 1797 5309584 5309951 9.060000e-117 431.0
40 TraesCS2D01G014500 chr2A 83.712 264 41 2 4290 4552 553431957 553432219 9.800000e-62 248.0
41 TraesCS2D01G014500 chr2A 84.274 248 38 1 4314 4561 659153717 659153471 1.640000e-59 241.0
42 TraesCS2D01G014500 chr2A 83.665 251 25 9 993 1227 5486853 5486603 5.940000e-54 222.0
43 TraesCS2D01G014500 chr4B 82.093 497 63 22 4062 4553 610124644 610125119 7.110000e-108 401.0
44 TraesCS2D01G014500 chr6D 79.842 506 73 20 4062 4561 102977667 102978149 4.370000e-90 342.0
45 TraesCS2D01G014500 chr4A 80.597 469 68 17 4095 4561 715695939 715695492 1.570000e-89 340.0
46 TraesCS2D01G014500 chr4A 83.146 178 25 3 4077 4254 659161920 659161748 1.700000e-34 158.0
47 TraesCS2D01G014500 chr4A 90.769 65 5 1 1330 1393 618286350 618286286 8.130000e-13 86.1
48 TraesCS2D01G014500 chr3D 78.685 502 70 19 4062 4561 528904244 528904710 2.670000e-77 300.0
49 TraesCS2D01G014500 chr3D 83.043 230 34 5 305 531 50007338 50007111 2.150000e-48 204.0
50 TraesCS2D01G014500 chr3D 86.076 79 6 2 1329 1406 61570537 61570611 3.780000e-11 80.5
51 TraesCS2D01G014500 chr6B 78.367 490 78 18 4065 4553 333536303 333535841 4.460000e-75 292.0
52 TraesCS2D01G014500 chr7D 78.486 502 65 19 4062 4561 54938952 54939412 5.770000e-74 289.0
53 TraesCS2D01G014500 chr7D 83.704 270 39 2 279 543 187210320 187210051 2.720000e-62 250.0
54 TraesCS2D01G014500 chr5D 80.965 373 59 11 4183 4553 116600616 116600254 7.470000e-73 285.0
55 TraesCS2D01G014500 chr5D 81.275 251 37 8 285 531 512749448 512749692 1.290000e-45 195.0
56 TraesCS2D01G014500 chr5D 82.938 211 30 5 4062 4269 522208515 522208308 7.790000e-43 185.0
57 TraesCS2D01G014500 chr5D 89.041 73 6 1 1330 1400 332041713 332041785 6.280000e-14 89.8
58 TraesCS2D01G014500 chr5B 84.615 247 35 2 4307 4553 84607 84850 4.560000e-60 243.0
59 TraesCS2D01G014500 chr5B 88.462 182 21 0 348 529 167294658 167294839 2.140000e-53 220.0
60 TraesCS2D01G014500 chr7A 82.836 268 31 10 279 531 108822388 108822655 4.590000e-55 226.0
61 TraesCS2D01G014500 chr3B 86.935 199 24 1 4062 4260 262085814 262085618 5.940000e-54 222.0
62 TraesCS2D01G014500 chr3B 87.324 71 7 1 1332 1400 748463069 748462999 3.780000e-11 80.5
63 TraesCS2D01G014500 chr1B 80.000 310 51 10 4065 4370 582341873 582341571 7.680000e-53 219.0
64 TraesCS2D01G014500 chr1B 81.028 253 44 4 281 531 610012975 610012725 1.000000e-46 198.0
65 TraesCS2D01G014500 chr3A 81.961 255 43 3 279 531 625037594 625037847 3.570000e-51 213.0
66 TraesCS2D01G014500 chr1D 84.831 178 22 3 4077 4254 42749673 42749501 1.690000e-39 174.0
67 TraesCS2D01G014500 chr1D 91.026 78 6 1 1330 1406 458142915 458142838 2.240000e-18 104.0
68 TraesCS2D01G014500 chr1D 92.958 71 5 0 1330 1400 458142856 458142926 2.240000e-18 104.0
69 TraesCS2D01G014500 chr1D 88.158 76 5 3 1329 1400 253207944 253207869 2.260000e-13 87.9


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 TraesCS2D01G014500 chr2D 7071239 7075799 4560 True 8423.000000 8423 100.000000 1 4561 1 chr2D.!!$R1 4560
1 TraesCS2D01G014500 chr2D 7064771 7066374 1603 False 1221.000000 1221 80.999000 2007 3596 1 chr2D.!!$F1 1589
2 TraesCS2D01G014500 chr2D 7085282 7093073 7791 True 1079.000000 2547 84.163750 940 3622 4 chr2D.!!$R3 2682
3 TraesCS2D01G014500 chr2D 7000522 7003712 3190 False 598.333333 1168 83.082667 930 3621 3 chr2D.!!$F4 2691
4 TraesCS2D01G014500 chr2B 2234421 2238381 3960 False 1701.000000 3120 93.343333 1 3901 3 chr2B.!!$F5 3900
5 TraesCS2D01G014500 chr2B 2501158 2505014 3856 True 1329.500000 3105 89.387000 1 3901 4 chr2B.!!$R3 3900
6 TraesCS2D01G014500 chr2B 2218375 2220859 2484 False 1208.000000 1954 87.611500 1416 3621 2 chr2B.!!$F4 2205
7 TraesCS2D01G014500 chr2B 2511208 2512957 1749 True 973.000000 1227 87.945000 1851 3621 2 chr2B.!!$R4 1770
8 TraesCS2D01G014500 chr2B 2250899 2251475 576 False 832.000000 832 92.612000 3903 4484 1 chr2B.!!$F1 581
9 TraesCS2D01G014500 chr2B 2131345 2136342 4997 False 640.500000 1040 84.053000 964 3597 2 chr2B.!!$F3 2633
10 TraesCS2D01G014500 chr2B 2344605 2348049 3444 True 622.666667 1201 82.843667 819 3607 3 chr2B.!!$R2 2788
11 TraesCS2D01G014500 chr2B 2523079 2527654 4575 True 512.000000 1162 85.420667 978 3597 3 chr2B.!!$R5 2619
12 TraesCS2D01G014500 chr2B 2269013 2269885 872 True 444.000000 444 76.663000 2706 3596 1 chr2B.!!$R1 890
13 TraesCS2D01G014500 chr2A 5483023 5486853 3830 True 1487.000000 2752 85.286500 993 3891 2 chr2A.!!$R2 2898
14 TraesCS2D01G014500 chr2A 5309584 5311995 2411 False 813.000000 1195 84.423500 1435 3607 2 chr2A.!!$F3 2172
15 TraesCS2D01G014500 chr2A 5526126 5528353 2227 True 807.500000 1175 85.501500 1457 3622 2 chr2A.!!$R3 2165

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
895 1063 1.497991 CTCCAGTACACACACAACCG 58.502 55.000 0.0 0.0 0.0 4.44 F
1156 1354 0.037232 GACCACCGAGTTCCTCAAGG 60.037 60.000 0.0 0.0 0.0 3.61 F
1880 4030 4.248859 CCAACCTCAGAACTATCACACAG 58.751 47.826 0.0 0.0 0.0 3.66 F
2608 4931 1.013596 CGATATTGTTCTTGCGGGCA 58.986 50.000 0.0 0.0 0.0 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1952 4187 1.618343 CAACAACCACTTTGGATCCCC 59.382 52.381 9.9 0.0 40.96 4.81 R
2354 4658 2.032620 GAATAGAAGACCTCCGCTCCA 58.967 52.381 0.0 0.0 0.00 3.86 R
3256 5667 0.098728 GAAATGTGGGTGCGATTCCG 59.901 55.000 0.0 0.0 39.16 4.30 R
4514 14129 0.244721 GAAGTGCCTTTGGTCATGGC 59.755 55.000 0.0 0.0 46.26 4.40 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
118 120 7.862274 TGAAGGACTGATATTGTATGGATCT 57.138 36.000 0.00 0.00 0.00 2.75
128 130 4.689612 TTGTATGGATCTAACCCAGCTC 57.310 45.455 0.00 0.00 37.08 4.09
129 131 3.653164 TGTATGGATCTAACCCAGCTCA 58.347 45.455 0.00 0.00 37.08 4.26
191 199 4.060038 TGTGATTCTCTCCTTAATCGCC 57.940 45.455 0.00 0.00 40.34 5.54
208 274 4.330944 TCGCCGAGTATTAAATGGATGT 57.669 40.909 0.00 0.00 0.00 3.06
228 294 9.483916 TGGATGTTAATTACCAATCTACATACG 57.516 33.333 0.00 0.00 32.37 3.06
229 295 9.701098 GGATGTTAATTACCAATCTACATACGA 57.299 33.333 0.00 0.00 30.02 3.43
240 306 6.865726 CCAATCTACATACGATTCTCTCCTTG 59.134 42.308 0.00 0.00 0.00 3.61
251 317 2.281761 CTCCTTGTGGCCGTGCTT 60.282 61.111 0.00 0.00 0.00 3.91
257 323 3.050275 GTGGCCGTGCTTGAGGAC 61.050 66.667 0.00 0.00 35.66 3.85
286 352 2.632377 CTCTTTTGGCGATTAGGCTGA 58.368 47.619 0.00 0.00 46.88 4.26
295 361 3.575630 GCGATTAGGCTGATCGTAATGA 58.424 45.455 32.97 0.00 45.99 2.57
468 547 9.367160 TCAACCCTCTCTTTCTTCATTTATTTT 57.633 29.630 0.00 0.00 0.00 1.82
490 569 7.514784 TTTTATGCCATCTCATCACTATTGG 57.485 36.000 0.00 0.00 0.00 3.16
506 585 2.495809 TGGCTAGTTGGCATGCATG 58.504 52.632 22.70 22.70 46.76 4.06
516 595 4.347876 AGTTGGCATGCATGATACTACCTA 59.652 41.667 30.64 13.97 0.00 3.08
556 661 5.332656 GGACAATCTTATTCTCGTCGAATGC 60.333 44.000 11.24 0.00 42.22 3.56
569 674 5.348164 TCGTCGAATGCAGAGAATTAATGA 58.652 37.500 0.00 0.00 0.00 2.57
570 675 5.810074 TCGTCGAATGCAGAGAATTAATGAA 59.190 36.000 0.00 0.00 0.00 2.57
574 679 6.481313 TCGAATGCAGAGAATTAATGAAGAGG 59.519 38.462 0.00 0.00 0.00 3.69
580 685 9.857656 TGCAGAGAATTAATGAAGAGGATTAAT 57.142 29.630 0.00 0.00 37.51 1.40
594 699 9.182933 GAAGAGGATTAATACATAGTTCGTGTC 57.817 37.037 0.00 0.00 0.00 3.67
615 720 7.567952 CGTGTCGACAAAACAATACAACATAGA 60.568 37.037 21.95 0.00 0.00 1.98
616 721 7.529519 GTGTCGACAAAACAATACAACATAGAC 59.470 37.037 21.95 0.00 0.00 2.59
633 744 2.787994 AGACAAATCTGAACAGCCAGG 58.212 47.619 0.00 0.00 34.99 4.45
636 747 4.072131 GACAAATCTGAACAGCCAGGTTA 58.928 43.478 0.00 0.00 36.55 2.85
642 753 2.936498 CTGAACAGCCAGGTTAATACGG 59.064 50.000 0.00 0.00 0.00 4.02
689 851 4.712337 TCCAACCCAACTCTTGCTTTTAAA 59.288 37.500 0.00 0.00 0.00 1.52
721 883 7.035838 TGGAGATGGAGATGGAGATTACCTATA 60.036 40.741 0.00 0.00 0.00 1.31
802 964 9.658475 CTATACAAGTGATTCTCTTCTTAGTCG 57.342 37.037 0.00 0.00 0.00 4.18
811 973 3.808726 TCTCTTCTTAGTCGCCGAGTATC 59.191 47.826 1.95 0.00 0.00 2.24
826 988 3.483574 CGAGTATCAAATGTTGTGGCGTC 60.484 47.826 0.00 0.00 33.17 5.19
836 998 3.311110 GTGGCGTCTGTCCTCCCA 61.311 66.667 0.00 0.00 0.00 4.37
837 999 2.997315 TGGCGTCTGTCCTCCCAG 60.997 66.667 0.00 0.00 0.00 4.45
840 1002 2.681778 CGTCTGTCCTCCCAGCCT 60.682 66.667 0.00 0.00 32.32 4.58
895 1063 1.497991 CTCCAGTACACACACAACCG 58.502 55.000 0.00 0.00 0.00 4.44
902 1071 3.942748 AGTACACACACAACCGAAACAAT 59.057 39.130 0.00 0.00 0.00 2.71
918 1087 5.406780 CGAAACAATACTTCTTGCTGAGACT 59.593 40.000 0.00 0.00 33.02 3.24
924 1093 3.230134 ACTTCTTGCTGAGACTGAGACT 58.770 45.455 0.00 0.00 33.02 3.24
928 1097 2.586648 TGCTGAGACTGAGACTACCA 57.413 50.000 0.00 0.00 0.00 3.25
1156 1354 0.037232 GACCACCGAGTTCCTCAAGG 60.037 60.000 0.00 0.00 0.00 3.61
1248 2101 7.116233 GGTTGACATGATGTTGTATTTTTGGAC 59.884 37.037 0.00 0.00 0.00 4.02
1255 2108 7.592938 TGATGTTGTATTTTTGGACATGTCTC 58.407 34.615 24.50 15.19 31.59 3.36
1670 3473 4.764771 ATGCGGGGTGCCATGCTT 62.765 61.111 5.71 0.00 45.60 3.91
1826 3812 5.812127 GTCACCAAAGAAATGCTCACTTTTT 59.188 36.000 0.00 0.00 32.59 1.94
1828 3814 5.043248 ACCAAAGAAATGCTCACTTTTTCG 58.957 37.500 0.00 0.00 35.14 3.46
1838 3824 9.744468 AAATGCTCACTTTTTCGTACTATTTTT 57.256 25.926 0.00 0.00 0.00 1.94
1880 4030 4.248859 CCAACCTCAGAACTATCACACAG 58.751 47.826 0.00 0.00 0.00 3.66
1943 4178 4.332819 ACACACTCAAACTTGTAACTCAGC 59.667 41.667 0.00 0.00 0.00 4.26
2564 4868 2.168521 CACGGGCTCTCCAAGATCTTAA 59.831 50.000 7.86 0.00 34.36 1.85
2608 4931 1.013596 CGATATTGTTCTTGCGGGCA 58.986 50.000 0.00 0.00 0.00 5.36
2717 5041 5.671735 TCTTGATATCAGGAAGGGGAAATCA 59.328 40.000 14.66 0.00 0.00 2.57
2810 5143 4.935702 ACACACACAAAAATGATGTCAGG 58.064 39.130 0.00 0.00 0.00 3.86
3495 5920 1.219393 GAGGAGGAAGGCAGGAACG 59.781 63.158 0.00 0.00 0.00 3.95
3520 10702 2.691252 GAGATTCCCCCGGGTGGT 60.691 66.667 21.85 5.25 36.47 4.16
3557 10741 7.324178 GGCTACATATCCGAGTTCAAGATTAT 58.676 38.462 0.00 0.00 0.00 1.28
3559 10743 9.856488 GCTACATATCCGAGTTCAAGATTATTA 57.144 33.333 0.00 0.00 0.00 0.98
3710 10929 9.438228 GCTAATTAGGGAATAATTGAGGTAGAC 57.562 37.037 14.28 0.00 42.73 2.59
3924 11214 5.365895 AGGTGTTATCCTTGTACATAGGGAC 59.634 44.000 18.28 15.29 33.52 4.46
3940 11230 6.156256 ACATAGGGACTTGTTGTAATGCTCTA 59.844 38.462 0.00 0.00 41.75 2.43
3962 11291 5.847111 ATTGAATGTAGCATCAGCACAAT 57.153 34.783 0.00 0.00 45.49 2.71
3966 11295 3.615224 TGTAGCATCAGCACAATGAGA 57.385 42.857 0.00 0.00 45.49 3.27
3968 11297 2.484742 AGCATCAGCACAATGAGACA 57.515 45.000 0.00 0.00 45.49 3.41
4057 11386 2.509964 GGTATTTGAGATCTGGTGGGGT 59.490 50.000 0.00 0.00 0.00 4.95
4075 11445 1.066929 GGTGTTGCTTGGCCCATTAAG 60.067 52.381 0.00 0.00 0.00 1.85
4083 11453 4.160252 TGCTTGGCCCATTAAGAATTTCTC 59.840 41.667 0.00 0.00 0.00 2.87
4114 11484 3.023832 AGTGGCCCATGTGTAAAATAGC 58.976 45.455 0.00 0.00 0.00 2.97
4131 11501 6.481954 AAATAGCAAGTGGTCGTTCTAAAG 57.518 37.500 0.00 0.00 0.00 1.85
4158 11528 0.321653 CCACCCCGAAAGTTGAGGAG 60.322 60.000 0.00 0.00 0.00 3.69
4219 11589 2.918712 AAGTGGTGTGTTGAGGAGAG 57.081 50.000 0.00 0.00 0.00 3.20
4259 11918 2.811317 GCTCGCTCACCTTGTCGG 60.811 66.667 0.00 0.00 39.35 4.79
4344 13148 0.101759 TGATCCGACGAAATCCGGTC 59.898 55.000 0.00 0.00 45.48 4.79
4380 13255 2.545742 GGCGCAACTTCCTTTTGTCATT 60.546 45.455 10.83 0.00 0.00 2.57
4381 13256 3.123050 GCGCAACTTCCTTTTGTCATTT 58.877 40.909 0.30 0.00 0.00 2.32
4382 13257 3.555547 GCGCAACTTCCTTTTGTCATTTT 59.444 39.130 0.30 0.00 0.00 1.82
4383 13258 4.742659 GCGCAACTTCCTTTTGTCATTTTA 59.257 37.500 0.30 0.00 0.00 1.52
4425 13417 9.651718 GCAGATAAGTTAATTATTTCTTGTCCG 57.348 33.333 13.29 8.48 34.10 4.79
4464 14079 5.050490 AGAATCCAAGTCGGTTTGATATCG 58.950 41.667 0.00 0.00 35.57 2.92
4490 14105 2.460330 GACACAATGTCGCCTCTGG 58.540 57.895 0.00 0.00 37.67 3.86
4491 14106 0.320771 GACACAATGTCGCCTCTGGT 60.321 55.000 0.00 0.00 37.67 4.00
4492 14107 0.973632 ACACAATGTCGCCTCTGGTA 59.026 50.000 0.00 0.00 0.00 3.25
4493 14108 1.337823 ACACAATGTCGCCTCTGGTAC 60.338 52.381 0.00 0.00 0.00 3.34
4494 14109 1.066858 CACAATGTCGCCTCTGGTACT 60.067 52.381 0.00 0.00 0.00 2.73
4495 14110 2.165641 CACAATGTCGCCTCTGGTACTA 59.834 50.000 0.00 0.00 0.00 1.82
4503 14118 8.998277 ATGTCGCCTCTGGTACTATTATATAT 57.002 34.615 0.00 0.00 0.00 0.86
4517 14132 8.786710 ACTATTATATATATTGGTACCGGCCA 57.213 34.615 7.57 0.00 36.62 5.36
4518 14133 9.388672 ACTATTATATATATTGGTACCGGCCAT 57.611 33.333 7.57 0.50 38.48 4.40
4519 14134 9.653287 CTATTATATATATTGGTACCGGCCATG 57.347 37.037 7.57 0.00 38.48 3.66
4520 14135 7.678207 TTATATATATTGGTACCGGCCATGA 57.322 36.000 7.57 0.00 38.48 3.07
4521 14136 2.561478 ATATTGGTACCGGCCATGAC 57.439 50.000 7.57 0.00 38.48 3.06
4523 14138 1.567208 ATTGGTACCGGCCATGACCA 61.567 55.000 14.16 14.16 40.21 4.02
4524 14139 2.224877 TGGTACCGGCCATGACCAA 61.225 57.895 15.46 2.15 39.01 3.67
4525 14140 1.001887 GGTACCGGCCATGACCAAA 60.002 57.895 0.00 0.00 31.89 3.28
4526 14141 1.029947 GGTACCGGCCATGACCAAAG 61.030 60.000 0.00 0.00 31.89 2.77
4527 14142 1.029947 GTACCGGCCATGACCAAAGG 61.030 60.000 0.00 0.00 0.00 3.11
4544 14159 2.052782 AGGCACTTCGAAAAACACCT 57.947 45.000 0.00 0.00 27.25 4.00
4546 14161 3.139077 AGGCACTTCGAAAAACACCTAG 58.861 45.455 0.00 0.00 27.25 3.02
4548 14163 2.225727 GCACTTCGAAAAACACCTAGGG 59.774 50.000 14.81 4.64 0.00 3.53
4549 14164 3.473625 CACTTCGAAAAACACCTAGGGT 58.526 45.455 14.81 5.35 35.62 4.34
4551 14166 4.337274 CACTTCGAAAAACACCTAGGGTTT 59.663 41.667 14.81 16.62 39.99 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 7.502226 ACCTTAATCATCGCCATTAATTCTCAA 59.498 33.333 0.00 0.00 0.00 3.02
64 66 4.672587 AATCTAGCGGCTCAGATTTGTA 57.327 40.909 19.77 0.00 38.10 2.41
161 169 4.260170 AGGAGAGAATCACATGCAGTTTC 58.740 43.478 0.00 0.00 37.82 2.78
228 294 0.250513 ACGGCCACAAGGAGAGAATC 59.749 55.000 2.24 0.00 36.89 2.52
229 295 0.036010 CACGGCCACAAGGAGAGAAT 60.036 55.000 2.24 0.00 36.89 2.40
240 306 3.050275 GTCCTCAAGCACGGCCAC 61.050 66.667 2.24 0.00 0.00 5.01
257 323 4.107051 CCAAAAGAGGGCGCGCAG 62.107 66.667 34.42 10.87 0.00 5.18
368 447 9.716507 GTCATGCACGACAATAAATAAACTATT 57.283 29.630 8.27 0.00 35.88 1.73
490 569 3.144506 AGTATCATGCATGCCAACTAGC 58.855 45.455 22.25 5.89 0.00 3.42
531 610 4.976224 TCGACGAGAATAAGATTGTCCA 57.024 40.909 0.00 0.00 0.00 4.02
543 622 3.510388 ATTCTCTGCATTCGACGAGAA 57.490 42.857 14.08 14.08 43.98 2.87
544 623 3.510388 AATTCTCTGCATTCGACGAGA 57.490 42.857 0.00 0.00 0.00 4.04
545 624 5.460091 TCATTAATTCTCTGCATTCGACGAG 59.540 40.000 0.00 0.00 0.00 4.18
569 674 7.861372 CGACACGAACTATGTATTAATCCTCTT 59.139 37.037 0.00 0.00 0.00 2.85
570 675 7.228108 TCGACACGAACTATGTATTAATCCTCT 59.772 37.037 0.00 0.00 31.06 3.69
574 679 7.903452 TGTCGACACGAACTATGTATTAATC 57.097 36.000 15.76 0.00 37.72 1.75
580 685 5.280164 TGTTTTGTCGACACGAACTATGTA 58.720 37.500 29.32 15.83 37.72 2.29
589 694 4.579564 TGTTGTATTGTTTTGTCGACACG 58.420 39.130 19.90 0.00 0.00 4.49
594 699 8.775220 TTTGTCTATGTTGTATTGTTTTGTCG 57.225 30.769 0.00 0.00 0.00 4.35
615 720 2.664402 ACCTGGCTGTTCAGATTTGT 57.336 45.000 3.84 0.00 36.93 2.83
616 721 5.649782 ATTAACCTGGCTGTTCAGATTTG 57.350 39.130 3.84 0.00 36.93 2.32
633 744 5.751243 ATCAGCCATTCAACCGTATTAAC 57.249 39.130 0.00 0.00 0.00 2.01
636 747 5.278463 GCAATATCAGCCATTCAACCGTATT 60.278 40.000 0.00 0.00 0.00 1.89
642 753 4.098349 TCCAAGCAATATCAGCCATTCAAC 59.902 41.667 0.00 0.00 0.00 3.18
689 851 5.471424 TCTCCATCTCCATCTCCACTAATT 58.529 41.667 0.00 0.00 0.00 1.40
721 883 5.048921 CGATTAAGGAGAGAATTGCATGCAT 60.049 40.000 23.37 7.51 0.00 3.96
777 939 8.129840 GCGACTAAGAAGAGAATCACTTGTATA 58.870 37.037 0.00 0.00 37.82 1.47
778 940 6.975772 GCGACTAAGAAGAGAATCACTTGTAT 59.024 38.462 0.00 0.00 37.82 2.29
802 964 2.477863 GCCACAACATTTGATACTCGGC 60.478 50.000 0.00 0.00 0.00 5.54
811 973 1.334960 GGACAGACGCCACAACATTTG 60.335 52.381 0.00 0.00 0.00 2.32
826 988 2.243774 TAGGGAGGCTGGGAGGACAG 62.244 65.000 0.00 0.00 41.41 3.51
836 998 2.305052 GCCCGTTTTATATAGGGAGGCT 59.695 50.000 8.63 0.00 46.64 4.58
837 999 2.305052 AGCCCGTTTTATATAGGGAGGC 59.695 50.000 8.63 6.82 46.64 4.70
840 1002 3.325716 GTGGAGCCCGTTTTATATAGGGA 59.674 47.826 8.63 0.00 46.64 4.20
895 1063 6.425114 TCAGTCTCAGCAAGAAGTATTGTTTC 59.575 38.462 0.00 0.00 35.21 2.78
902 1071 4.402829 AGTCTCAGTCTCAGCAAGAAGTA 58.597 43.478 0.00 0.00 35.21 2.24
918 1087 0.972983 GGGCAGAGCTGGTAGTCTCA 60.973 60.000 0.00 0.00 0.00 3.27
1156 1354 2.203126 CATGAAGCTCGGCCCCTC 60.203 66.667 0.00 0.00 0.00 4.30
1248 2101 3.672808 AGCAAAGAGGTGAAGAGACATG 58.327 45.455 0.00 0.00 0.00 3.21
1255 2108 2.925306 GCATGCAAGCAAAGAGGTGAAG 60.925 50.000 14.21 0.00 0.00 3.02
1390 2516 3.391955 ACGCTAGTATAGTCCTCTGTCCT 59.608 47.826 0.00 0.00 41.93 3.85
1797 3600 5.932303 GTGAGCATTTCTTTGGTGACTACTA 59.068 40.000 0.00 0.00 30.08 1.82
1880 4030 8.958119 TGTCCCTAAGTGTGATATATCAAAAC 57.042 34.615 16.97 16.83 38.75 2.43
1931 4166 2.162681 CCCCCTTTGCTGAGTTACAAG 58.837 52.381 0.00 0.00 0.00 3.16
1952 4187 1.618343 CAACAACCACTTTGGATCCCC 59.382 52.381 9.90 0.00 40.96 4.81
1955 4190 2.622942 TCAGCAACAACCACTTTGGATC 59.377 45.455 0.00 0.00 40.96 3.36
2354 4658 2.032620 GAATAGAAGACCTCCGCTCCA 58.967 52.381 0.00 0.00 0.00 3.86
2717 5041 2.198703 TCGATGGCCTCCTCCGAT 59.801 61.111 3.32 0.00 0.00 4.18
3256 5667 0.098728 GAAATGTGGGTGCGATTCCG 59.901 55.000 0.00 0.00 39.16 4.30
3495 5920 0.536006 CGGGGGAATCTCAAGATGGC 60.536 60.000 0.00 0.00 34.49 4.40
3557 10741 5.163673 TGCGAAATGTATGCTGCAAGATTAA 60.164 36.000 6.36 0.00 34.07 1.40
3559 10743 3.129113 TGCGAAATGTATGCTGCAAGATT 59.871 39.130 6.36 4.07 34.07 2.40
3641 10830 7.001073 ACTCCCTCATTCCAAAATATAAGAGC 58.999 38.462 0.00 0.00 0.00 4.09
3710 10929 4.666655 CGAACGAAAATAACACAGGAGCAG 60.667 45.833 0.00 0.00 0.00 4.24
3924 11214 9.926751 CTACATTCAATAGAGCATTACAACAAG 57.073 33.333 0.00 0.00 0.00 3.16
3940 11230 5.358725 TCATTGTGCTGATGCTACATTCAAT 59.641 36.000 0.00 0.00 40.48 2.57
3962 11291 1.589630 CCCACGACGGAATGTCTCA 59.410 57.895 0.00 0.00 45.87 3.27
3966 11295 3.632080 TGCCCCACGACGGAATGT 61.632 61.111 0.00 0.00 36.56 2.71
3968 11297 4.404098 GGTGCCCCACGACGGAAT 62.404 66.667 0.00 0.00 36.56 3.01
3987 11316 0.368907 CGGTGTTAAGAACGATGGCG 59.631 55.000 3.56 0.00 44.79 5.69
3991 11320 1.338389 CCCACCGGTGTTAAGAACGAT 60.338 52.381 31.80 0.00 0.00 3.73
4057 11386 2.300956 TCTTAATGGGCCAAGCAACA 57.699 45.000 11.89 0.00 0.00 3.33
4075 11445 5.866092 GGCCACTTTGAGATTTGAGAAATTC 59.134 40.000 0.00 0.00 0.00 2.17
4083 11453 2.564062 ACATGGGCCACTTTGAGATTTG 59.436 45.455 9.28 0.74 0.00 2.32
4097 11467 4.423732 CACTTGCTATTTTACACATGGGC 58.576 43.478 0.00 0.00 0.00 5.36
4114 11484 6.073927 GGACTAAACTTTAGAACGACCACTTG 60.074 42.308 14.37 0.00 0.00 3.16
4131 11501 1.072806 ACTTTCGGGGTGGGACTAAAC 59.927 52.381 0.00 0.00 0.00 2.01
4158 11528 6.276847 CCACTATACAAAGAGATCTCACACC 58.723 44.000 24.39 0.00 0.00 4.16
4196 11566 5.071788 TCTCTCCTCAACACACCACTTAAAT 59.928 40.000 0.00 0.00 0.00 1.40
4219 11589 2.000447 GTGCGTGTGGTCTCCTATTTC 59.000 52.381 0.00 0.00 0.00 2.17
4259 11918 2.266689 CATGCCCTTGCCTTTGCC 59.733 61.111 0.00 0.00 36.33 4.52
4425 13417 8.628280 ACTTGGATTCTAAGTCGTATACTTACC 58.372 37.037 9.41 0.00 46.85 2.85
4452 14067 1.122501 CGCGATCACGATATCAAACCG 59.877 52.381 0.00 0.90 42.66 4.44
4464 14079 3.858040 GACATTGTGTCGCGATCAC 57.142 52.632 25.11 25.11 37.67 3.06
4491 14106 9.880254 TGGCCGGTACCAATATATATAATAGTA 57.120 33.333 13.54 0.00 36.55 1.82
4492 14107 8.786710 TGGCCGGTACCAATATATATAATAGT 57.213 34.615 13.54 0.00 36.55 2.12
4493 14108 9.653287 CATGGCCGGTACCAATATATATAATAG 57.347 37.037 13.54 0.00 44.65 1.73
4494 14109 9.382307 TCATGGCCGGTACCAATATATATAATA 57.618 33.333 13.54 0.00 44.65 0.98
4495 14110 8.154856 GTCATGGCCGGTACCAATATATATAAT 58.845 37.037 13.54 0.00 44.65 1.28
4503 14118 0.470766 GGTCATGGCCGGTACCAATA 59.529 55.000 13.54 0.00 44.65 1.90
4504 14119 1.226262 GGTCATGGCCGGTACCAAT 59.774 57.895 13.54 0.00 44.65 3.16
4507 14122 1.001887 TTTGGTCATGGCCGGTACC 60.002 57.895 12.67 12.15 0.00 3.34
4508 14123 1.029947 CCTTTGGTCATGGCCGGTAC 61.030 60.000 12.67 0.00 0.00 3.34
4509 14124 1.301623 CCTTTGGTCATGGCCGGTA 59.698 57.895 12.67 0.00 0.00 4.02
4511 14126 3.451894 GCCTTTGGTCATGGCCGG 61.452 66.667 12.67 8.20 40.71 6.13
4513 14128 1.187567 AAGTGCCTTTGGTCATGGCC 61.188 55.000 10.20 10.20 45.56 5.36
4514 14129 0.244721 GAAGTGCCTTTGGTCATGGC 59.755 55.000 0.00 0.00 46.26 4.40
4515 14130 0.523072 CGAAGTGCCTTTGGTCATGG 59.477 55.000 0.00 0.00 0.00 3.66
4516 14131 1.522668 TCGAAGTGCCTTTGGTCATG 58.477 50.000 0.00 0.00 0.00 3.07
4517 14132 2.270352 TTCGAAGTGCCTTTGGTCAT 57.730 45.000 0.00 0.00 0.00 3.06
4518 14133 2.045561 TTTCGAAGTGCCTTTGGTCA 57.954 45.000 0.00 0.00 0.00 4.02
4519 14134 3.113322 GTTTTTCGAAGTGCCTTTGGTC 58.887 45.455 0.00 0.00 0.00 4.02
4520 14135 2.494073 TGTTTTTCGAAGTGCCTTTGGT 59.506 40.909 0.00 0.00 0.00 3.67
4521 14136 2.857748 GTGTTTTTCGAAGTGCCTTTGG 59.142 45.455 0.00 0.00 0.00 3.28
4523 14138 2.758423 AGGTGTTTTTCGAAGTGCCTTT 59.242 40.909 0.00 0.00 0.00 3.11
4524 14139 2.375146 AGGTGTTTTTCGAAGTGCCTT 58.625 42.857 0.00 0.00 0.00 4.35
4525 14140 2.052782 AGGTGTTTTTCGAAGTGCCT 57.947 45.000 0.00 0.73 0.00 4.75
4526 14141 2.225727 CCTAGGTGTTTTTCGAAGTGCC 59.774 50.000 0.00 0.00 0.00 5.01
4527 14142 2.225727 CCCTAGGTGTTTTTCGAAGTGC 59.774 50.000 8.29 0.00 0.00 4.40
4528 14143 3.473625 ACCCTAGGTGTTTTTCGAAGTG 58.526 45.455 8.29 0.00 32.98 3.16
4529 14144 3.851458 ACCCTAGGTGTTTTTCGAAGT 57.149 42.857 8.29 0.00 32.98 3.01
4530 14145 5.509716 AAAACCCTAGGTGTTTTTCGAAG 57.490 39.130 24.20 4.15 41.75 3.79


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

AutoCloner maintained by Alex Coulton.