Multiple sequence alignment - TraesCS4D01G003900

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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 TraesCS4D01G003900 chr4D 100.000 4294 0 0 1 4294 1665001 1669294 0.000000e+00 7930.0
1 TraesCS4D01G003900 chr4D 85.662 1367 185 7 2079 3439 2999497 3000858 0.000000e+00 1428.0
2 TraesCS4D01G003900 chr4D 98.077 52 1 0 4104 4155 36551441 36551390 1.640000e-14 91.6
3 TraesCS4D01G003900 chr4A 94.089 2081 115 3 2016 4095 603036893 603038966 0.000000e+00 3155.0
4 TraesCS4D01G003900 chr4A 85.660 1325 147 23 365 1667 603034129 603035432 0.000000e+00 1354.0
5 TraesCS4D01G003900 chr4A 86.103 331 35 1 1 320 603033801 603034131 3.180000e-91 346.0
6 TraesCS4D01G003900 chr4A 95.522 134 5 1 4138 4271 603039375 603039507 3.360000e-51 213.0
7 TraesCS4D01G003900 chrUn 89.846 2019 160 16 1246 3244 47922565 47920572 0.000000e+00 2551.0
8 TraesCS4D01G003900 chrUn 82.122 867 109 20 3238 4087 47920501 47919664 0.000000e+00 701.0
9 TraesCS4D01G003900 chrUn 89.062 64 7 0 1585 1648 47478761 47478824 3.560000e-11 80.5
10 TraesCS4D01G003900 chrUn 96.875 32 1 0 4262 4293 39801066 39801035 2.000000e-03 54.7
11 TraesCS4D01G003900 chrUn 96.875 32 1 0 4262 4293 300441842 300441811 2.000000e-03 54.7
12 TraesCS4D01G003900 chr3D 88.229 1835 180 13 2016 3829 567742613 567740794 0.000000e+00 2159.0
13 TraesCS4D01G003900 chr3D 85.480 1708 185 24 1 1670 567747069 567745387 0.000000e+00 1722.0
14 TraesCS4D01G003900 chr3D 96.875 32 1 0 4262 4293 271484555 271484586 2.000000e-03 54.7
15 TraesCS4D01G003900 chr6D 86.743 1305 160 6 2076 3374 21078559 21079856 0.000000e+00 1439.0
16 TraesCS4D01G003900 chr5D 84.527 1312 183 12 2083 3393 447388098 447386806 0.000000e+00 1280.0
17 TraesCS4D01G003900 chr5D 73.050 1013 173 52 732 1705 447305992 447305041 2.550000e-67 267.0
18 TraesCS4D01G003900 chr5A 83.371 1311 187 23 2057 3350 565249416 565250712 0.000000e+00 1184.0
19 TraesCS4D01G003900 chr5A 73.427 572 113 29 736 1294 565248050 565248595 1.230000e-40 178.0
20 TraesCS4D01G003900 chr5B 83.678 1256 195 7 2083 3335 545279651 545280899 0.000000e+00 1175.0
21 TraesCS4D01G003900 chr5B 82.486 1239 206 8 2078 3309 545818775 545820009 0.000000e+00 1075.0
22 TraesCS4D01G003900 chr5B 77.364 645 108 20 732 1359 545278397 545279020 8.840000e-92 348.0
23 TraesCS4D01G003900 chr5B 89.130 92 10 0 1576 1667 545279228 545279319 9.760000e-22 115.0
24 TraesCS4D01G003900 chr5B 92.105 76 6 0 1573 1648 545818296 545818371 1.630000e-19 108.0
25 TraesCS4D01G003900 chr5B 100.000 28 0 0 4266 4293 375947171 375947144 8.000000e-03 52.8


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 TraesCS4D01G003900 chr4D 1665001 1669294 4293 False 7930.0 7930 100.000000 1 4294 1 chr4D.!!$F1 4293
1 TraesCS4D01G003900 chr4D 2999497 3000858 1361 False 1428.0 1428 85.662000 2079 3439 1 chr4D.!!$F2 1360
2 TraesCS4D01G003900 chr4A 603033801 603039507 5706 False 1267.0 3155 90.343500 1 4271 4 chr4A.!!$F1 4270
3 TraesCS4D01G003900 chrUn 47919664 47922565 2901 True 1626.0 2551 85.984000 1246 4087 2 chrUn.!!$R3 2841
4 TraesCS4D01G003900 chr3D 567740794 567747069 6275 True 1940.5 2159 86.854500 1 3829 2 chr3D.!!$R1 3828
5 TraesCS4D01G003900 chr6D 21078559 21079856 1297 False 1439.0 1439 86.743000 2076 3374 1 chr6D.!!$F1 1298
6 TraesCS4D01G003900 chr5D 447386806 447388098 1292 True 1280.0 1280 84.527000 2083 3393 1 chr5D.!!$R2 1310
7 TraesCS4D01G003900 chr5D 447305041 447305992 951 True 267.0 267 73.050000 732 1705 1 chr5D.!!$R1 973
8 TraesCS4D01G003900 chr5A 565248050 565250712 2662 False 681.0 1184 78.399000 736 3350 2 chr5A.!!$F1 2614
9 TraesCS4D01G003900 chr5B 545818296 545820009 1713 False 591.5 1075 87.295500 1573 3309 2 chr5B.!!$F2 1736
10 TraesCS4D01G003900 chr5B 545278397 545280899 2502 False 546.0 1175 83.390667 732 3335 3 chr5B.!!$F1 2603

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
854 933 0.040425 GCGACAACAACGGAAGCAAT 60.040 50.0 0.00 0.0 0.00 3.56 F
1506 1646 0.036199 GCCATTTGCATTGCCCAGAA 60.036 50.0 6.12 0.0 40.77 3.02 F
1969 2273 0.319900 ACTAGTGCGTGCAACAGGAG 60.320 55.0 0.00 0.0 35.74 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2508 5327 0.110192 GCAAGTAACGGCACTTCTGC 60.110 55.000 1.32 1.26 43.41 4.26 R
2780 5605 2.020720 CCTTGCACCACAGTTGTTGTA 58.979 47.619 0.00 0.00 38.16 2.41 R
3877 6829 0.107800 CTCATCACCAGTCCCTGCTG 60.108 60.000 0.00 0.00 36.31 4.41 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
25 26 5.119279 CACCAAACAATCTCGACTCACTAAG 59.881 44.000 0.00 0.00 0.00 2.18
41 42 5.188434 TCACTAAGATTTCCAGCCAATCAG 58.812 41.667 0.00 0.00 33.67 2.90
49 50 7.723324 AGATTTCCAGCCAATCAGATAATTTG 58.277 34.615 0.00 0.00 33.67 2.32
66 67 3.827008 TTTGCATAGGTCTGGCTCTAG 57.173 47.619 0.00 0.00 0.00 2.43
167 168 7.821359 TCAAATAAGATGGATATGTAGCTCTGC 59.179 37.037 0.00 0.00 0.00 4.26
171 172 3.969287 TGGATATGTAGCTCTGCATCC 57.031 47.619 3.78 0.00 37.16 3.51
201 213 2.042843 AGGGCTAGGGACCACTCG 60.043 66.667 0.00 0.00 45.05 4.18
212 224 0.520404 GACCACTCGAACAGACGCTA 59.480 55.000 0.00 0.00 0.00 4.26
226 238 1.594862 GACGCTAGCTGGCTAATGTTG 59.405 52.381 20.56 4.92 0.00 3.33
229 241 1.601430 GCTAGCTGGCTAATGTTGCTC 59.399 52.381 15.78 0.00 35.47 4.26
273 285 2.809696 CGTACGAAAAATCACCCAACCT 59.190 45.455 10.44 0.00 0.00 3.50
278 290 2.358322 AAAATCACCCAACCTCGTGT 57.642 45.000 0.00 0.00 0.00 4.49
315 327 6.897259 TTTATTCTATCTTTCGTCGTTGGG 57.103 37.500 0.00 0.00 0.00 4.12
317 329 4.730949 TTCTATCTTTCGTCGTTGGGAT 57.269 40.909 0.00 0.00 0.00 3.85
318 330 5.840243 TTCTATCTTTCGTCGTTGGGATA 57.160 39.130 0.00 0.00 0.00 2.59
319 331 6.401047 TTCTATCTTTCGTCGTTGGGATAT 57.599 37.500 0.00 0.00 0.00 1.63
320 332 6.401047 TCTATCTTTCGTCGTTGGGATATT 57.599 37.500 0.00 0.00 0.00 1.28
321 333 7.514784 TCTATCTTTCGTCGTTGGGATATTA 57.485 36.000 0.00 0.00 0.00 0.98
322 334 7.944061 TCTATCTTTCGTCGTTGGGATATTAA 58.056 34.615 0.00 0.00 0.00 1.40
323 335 8.415553 TCTATCTTTCGTCGTTGGGATATTAAA 58.584 33.333 0.00 0.00 0.00 1.52
324 336 6.651755 TCTTTCGTCGTTGGGATATTAAAC 57.348 37.500 0.00 0.00 0.00 2.01
325 337 5.581874 TCTTTCGTCGTTGGGATATTAAACC 59.418 40.000 0.00 0.00 0.00 3.27
326 338 3.446799 TCGTCGTTGGGATATTAAACCG 58.553 45.455 0.00 0.00 0.00 4.44
327 339 3.119173 TCGTCGTTGGGATATTAAACCGT 60.119 43.478 0.00 0.00 0.00 4.83
328 340 3.243643 CGTCGTTGGGATATTAAACCGTC 59.756 47.826 0.00 0.00 0.00 4.79
329 341 4.183101 GTCGTTGGGATATTAAACCGTCA 58.817 43.478 0.00 0.00 0.00 4.35
330 342 4.812626 GTCGTTGGGATATTAAACCGTCAT 59.187 41.667 0.00 0.00 0.00 3.06
331 343 5.295045 GTCGTTGGGATATTAAACCGTCATT 59.705 40.000 0.00 0.00 0.00 2.57
332 344 5.881443 TCGTTGGGATATTAAACCGTCATTT 59.119 36.000 0.00 0.00 0.00 2.32
333 345 7.011295 GTCGTTGGGATATTAAACCGTCATTTA 59.989 37.037 0.00 0.00 0.00 1.40
334 346 7.716123 TCGTTGGGATATTAAACCGTCATTTAT 59.284 33.333 0.00 0.00 0.00 1.40
335 347 8.347035 CGTTGGGATATTAAACCGTCATTTATT 58.653 33.333 0.00 0.00 0.00 1.40
377 434 4.854291 CGAATGTAGCTATCCGAATGACTC 59.146 45.833 0.00 0.00 0.00 3.36
452 510 4.895668 ATTTTCTGCCCACATGAATGTT 57.104 36.364 0.00 0.00 39.39 2.71
458 516 1.747355 GCCCACATGAATGTTCTCAGG 59.253 52.381 0.00 0.00 39.39 3.86
508 567 7.219535 CAGTTCACTCAACACATTTTCAAAGAG 59.780 37.037 0.00 0.00 37.48 2.85
515 574 2.095059 CACATTTTCAAAGAGGGCCTCG 60.095 50.000 27.11 13.92 35.36 4.63
547 606 3.544285 GCGTTAGCGAGTGATATAGATGC 59.456 47.826 2.07 0.00 41.33 3.91
809 882 1.002134 CATGGGCCCGAAGAGTTGT 60.002 57.895 19.37 0.00 0.00 3.32
854 933 0.040425 GCGACAACAACGGAAGCAAT 60.040 50.000 0.00 0.00 0.00 3.56
881 963 2.786495 GCTTCTCCTCGGCGATGGA 61.786 63.158 21.24 21.24 0.00 3.41
893 975 2.114670 CGATGGAAGTGCCGGCATT 61.115 57.895 35.23 27.72 40.66 3.56
906 988 1.011968 CGGCATTTTCGAGGTCGTCA 61.012 55.000 0.00 0.00 40.80 4.35
908 990 1.128692 GGCATTTTCGAGGTCGTCAAG 59.871 52.381 0.00 0.00 40.80 3.02
934 1016 2.363788 GTGGAGAACACTACGATGCA 57.636 50.000 0.00 0.00 46.72 3.96
971 1053 1.134367 CTGCAAGCCATCAACATGAGG 59.866 52.381 0.00 0.00 30.57 3.86
980 1074 4.473520 AACATGAGGGGCGGCTCG 62.474 66.667 9.56 0.00 0.00 5.03
1001 1095 3.461773 CGGTGGAGCCTCGGTGAT 61.462 66.667 0.00 0.00 34.25 3.06
1047 1141 1.303643 AGGTTGCCCTACTTGCTGC 60.304 57.895 0.00 0.00 40.19 5.25
1055 1149 1.221840 CTACTTGCTGCACCCGGAT 59.778 57.895 0.73 0.00 0.00 4.18
1058 1152 1.675310 CTTGCTGCACCCGGATTCA 60.675 57.895 0.73 0.00 0.00 2.57
1064 1158 2.026641 CTGCACCCGGATTCAAATGAT 58.973 47.619 0.73 0.00 0.00 2.45
1167 1270 1.606313 CCCGGCTTTTGGTGATGGT 60.606 57.895 0.00 0.00 0.00 3.55
1175 1278 3.859118 TTGGTGATGGTGGTGGCGG 62.859 63.158 0.00 0.00 0.00 6.13
1178 1281 1.003112 GTGATGGTGGTGGCGGTAA 60.003 57.895 0.00 0.00 0.00 2.85
1183 1286 1.078918 GGTGGTGGCGGTAACCTAC 60.079 63.158 3.46 0.00 38.60 3.18
1189 1292 3.263937 TGGTGGCGGTAACCTACTTTATT 59.736 43.478 3.46 0.00 38.60 1.40
1190 1293 3.873361 GGTGGCGGTAACCTACTTTATTC 59.127 47.826 0.00 0.00 34.66 1.75
1191 1294 4.383444 GGTGGCGGTAACCTACTTTATTCT 60.383 45.833 0.00 0.00 34.66 2.40
1200 1303 5.871324 ACCTACTTTATTCTGGGGGAAAA 57.129 39.130 0.00 0.00 37.49 2.29
1206 1309 6.271537 ACTTTATTCTGGGGGAAAATCCAAT 58.728 36.000 0.00 0.00 38.64 3.16
1207 1310 7.426667 ACTTTATTCTGGGGGAAAATCCAATA 58.573 34.615 0.00 0.00 38.64 1.90
1368 1483 4.062991 GTTGGTTCGACTTAGACCACAAT 58.937 43.478 5.41 0.00 0.00 2.71
1415 1531 3.133901 TGGGAGGAAAACCAAAAAGAAGC 59.866 43.478 0.00 0.00 32.89 3.86
1503 1643 2.186602 CTGGCCATTTGCATTGCCCA 62.187 55.000 5.51 4.12 40.02 5.36
1506 1646 0.036199 GCCATTTGCATTGCCCAGAA 60.036 50.000 6.12 0.00 40.77 3.02
1732 2014 5.477510 TGAATTATTTGCGTTGCTTTCCAT 58.522 33.333 0.00 0.00 0.00 3.41
1741 2023 3.747193 CGTTGCTTTCCATATGTGTCAC 58.253 45.455 1.24 0.00 0.00 3.67
1742 2024 3.724716 CGTTGCTTTCCATATGTGTCACG 60.725 47.826 1.24 0.00 0.00 4.35
1743 2025 3.052455 TGCTTTCCATATGTGTCACGT 57.948 42.857 2.65 2.65 0.00 4.49
1755 2037 4.966965 TGTGTCACGTGGTTATTTTTGT 57.033 36.364 17.00 0.00 0.00 2.83
1769 2051 8.452534 TGGTTATTTTTGTTCGTGGACATATAC 58.547 33.333 0.00 0.00 0.00 1.47
1969 2273 0.319900 ACTAGTGCGTGCAACAGGAG 60.320 55.000 0.00 0.00 35.74 3.69
2014 2318 9.778741 TTCATTAGTTAATTATCTCGCTCCATT 57.221 29.630 0.00 0.00 0.00 3.16
2098 4915 3.769300 AGCTTGGGTTTAATCATTGGTCC 59.231 43.478 0.00 0.00 0.00 4.46
2152 4969 3.153919 TGGTTCTTGGTGCAATCCTAAC 58.846 45.455 0.00 0.00 0.00 2.34
2153 4970 3.181434 TGGTTCTTGGTGCAATCCTAACT 60.181 43.478 0.00 0.00 0.00 2.24
2168 4985 7.677982 GCAATCCTAACTATCCGTGGTTTTAAC 60.678 40.741 0.00 0.00 31.03 2.01
2206 5023 3.122111 GCGCTGAGACAGAAGTTCTTTAC 59.878 47.826 1.56 0.00 32.44 2.01
2289 5107 8.615240 GCGGATGCTCATCTCTTTAGAAGAGT 62.615 46.154 15.18 3.28 45.34 3.24
2342 5160 1.306141 CAGGCTAGGTGGAGGTGGA 60.306 63.158 0.00 0.00 0.00 4.02
2508 5327 1.811266 CGTGGATGTTGCCTCGAGG 60.811 63.158 27.83 27.83 45.07 4.63
2571 5390 1.874019 CTCGCCGACCATCTTCACG 60.874 63.158 0.00 0.00 0.00 4.35
2585 5404 0.887387 TTCACGCGGAAAAAGGAGGG 60.887 55.000 12.47 0.00 30.98 4.30
2791 5616 4.578928 GGATCAAACAGGTACAACAACTGT 59.421 41.667 0.00 0.00 46.59 3.55
2849 5674 7.605449 TGTATTATTATACTGGACGCCTAACC 58.395 38.462 3.72 0.00 37.97 2.85
2894 5719 6.016276 GCTTTGGAGTCCTTCTTGTTGAATTA 60.016 38.462 11.33 0.00 33.71 1.40
2994 5820 5.048852 GCAGAAGGCAATTTGGCAAAAATAA 60.049 36.000 23.07 0.00 46.46 1.40
3147 5973 1.019278 AGCACCCAATAAGCGTGTCG 61.019 55.000 0.00 0.00 0.00 4.35
3299 6213 5.123186 TGCAACATACCCTCGATAGTTTTTG 59.877 40.000 0.00 0.00 37.40 2.44
3508 6448 2.832129 TCCATCTTCCACACCTACTCAC 59.168 50.000 0.00 0.00 0.00 3.51
3586 6526 4.221924 TGTGTCGATCCTTGTCTCCATTAA 59.778 41.667 0.00 0.00 0.00 1.40
3740 6687 7.283127 CCAGAATGCAAACTATACCAACACTAT 59.717 37.037 0.00 0.00 31.97 2.12
3844 6796 1.315257 GGTTGCTGGCCCTACACATG 61.315 60.000 0.00 0.00 0.00 3.21
3845 6797 0.609131 GTTGCTGGCCCTACACATGT 60.609 55.000 0.00 0.00 0.00 3.21
3846 6798 0.988063 TTGCTGGCCCTACACATGTA 59.012 50.000 0.00 0.00 0.00 2.29
3847 6799 0.251916 TGCTGGCCCTACACATGTAC 59.748 55.000 0.00 0.00 0.00 2.90
3848 6800 0.251916 GCTGGCCCTACACATGTACA 59.748 55.000 0.00 0.00 0.00 2.90
3849 6801 1.134098 GCTGGCCCTACACATGTACAT 60.134 52.381 1.41 1.41 0.00 2.29
3877 6829 3.890128 TCTATGATTCGAGCGTGTGATC 58.110 45.455 0.00 0.00 0.00 2.92
3942 6894 0.672401 AGGTACATGGCGTGTTTCGG 60.672 55.000 18.82 0.00 42.29 4.30
3971 6923 0.820891 CTCCCAGCAGCAAACACACT 60.821 55.000 0.00 0.00 0.00 3.55
3986 6938 4.913335 ACACACTCGAGTCAAGTTTCTA 57.087 40.909 16.96 0.00 0.00 2.10
3988 6940 5.223382 ACACACTCGAGTCAAGTTTCTATG 58.777 41.667 16.96 2.20 0.00 2.23
4025 6977 3.077359 CTGTCCCTCAACAATCCACTTC 58.923 50.000 0.00 0.00 0.00 3.01
4072 7024 3.307691 CCATCTGACTACAACATGTGGGT 60.308 47.826 4.95 6.91 32.73 4.51
4092 7044 6.548321 TGGGTTACCATTGTTTCATTCTACT 58.452 36.000 2.98 0.00 43.37 2.57
4093 7045 6.657541 TGGGTTACCATTGTTTCATTCTACTC 59.342 38.462 2.98 0.00 43.37 2.59
4094 7046 6.884836 GGGTTACCATTGTTTCATTCTACTCT 59.115 38.462 2.98 0.00 36.50 3.24
4095 7047 8.044908 GGGTTACCATTGTTTCATTCTACTCTA 58.955 37.037 2.98 0.00 36.50 2.43
4096 7048 9.444600 GGTTACCATTGTTTCATTCTACTCTAA 57.555 33.333 0.00 0.00 0.00 2.10
4100 7052 8.462016 ACCATTGTTTCATTCTACTCTAATTGC 58.538 33.333 0.00 0.00 0.00 3.56
4101 7053 7.917505 CCATTGTTTCATTCTACTCTAATTGCC 59.082 37.037 0.00 0.00 0.00 4.52
4119 7457 3.793712 TGCCCTTCTAACTACCCTGTAA 58.206 45.455 0.00 0.00 0.00 2.41
4120 7458 4.368067 TGCCCTTCTAACTACCCTGTAAT 58.632 43.478 0.00 0.00 0.00 1.89
4121 7459 4.786454 TGCCCTTCTAACTACCCTGTAATT 59.214 41.667 0.00 0.00 0.00 1.40
4122 7460 5.104652 TGCCCTTCTAACTACCCTGTAATTC 60.105 44.000 0.00 0.00 0.00 2.17
4123 7461 5.686913 GCCCTTCTAACTACCCTGTAATTCC 60.687 48.000 0.00 0.00 0.00 3.01
4124 7462 5.163227 CCCTTCTAACTACCCTGTAATTCCC 60.163 48.000 0.00 0.00 0.00 3.97
4125 7463 5.163227 CCTTCTAACTACCCTGTAATTCCCC 60.163 48.000 0.00 0.00 0.00 4.81
4126 7464 5.230746 TCTAACTACCCTGTAATTCCCCT 57.769 43.478 0.00 0.00 0.00 4.79
4127 7465 4.966805 TCTAACTACCCTGTAATTCCCCTG 59.033 45.833 0.00 0.00 0.00 4.45
4128 7466 3.216230 ACTACCCTGTAATTCCCCTGT 57.784 47.619 0.00 0.00 0.00 4.00
4129 7467 4.357313 ACTACCCTGTAATTCCCCTGTA 57.643 45.455 0.00 0.00 0.00 2.74
4130 7468 4.702196 ACTACCCTGTAATTCCCCTGTAA 58.298 43.478 0.00 0.00 0.00 2.41
4131 7469 5.102967 ACTACCCTGTAATTCCCCTGTAAA 58.897 41.667 0.00 0.00 0.00 2.01
4132 7470 4.586306 ACCCTGTAATTCCCCTGTAAAG 57.414 45.455 0.00 0.00 0.00 1.85
4133 7471 3.288092 CCCTGTAATTCCCCTGTAAAGC 58.712 50.000 0.00 0.00 0.00 3.51
4134 7472 3.288092 CCTGTAATTCCCCTGTAAAGCC 58.712 50.000 0.00 0.00 0.00 4.35
4135 7473 3.288092 CTGTAATTCCCCTGTAAAGCCC 58.712 50.000 0.00 0.00 0.00 5.19
4136 7474 2.024751 TGTAATTCCCCTGTAAAGCCCC 60.025 50.000 0.00 0.00 0.00 5.80
4137 7475 1.089123 AATTCCCCTGTAAAGCCCCA 58.911 50.000 0.00 0.00 0.00 4.96
4179 7517 6.806751 TCTTCGCAGTCTTAGCAAATACTAT 58.193 36.000 0.00 0.00 0.00 2.12
4193 7531 7.930217 AGCAAATACTATTTACTCCGTACGTA 58.070 34.615 15.21 0.00 0.00 3.57
4211 7549 4.783621 TGCGCCCATGCAGAGACC 62.784 66.667 4.18 0.00 40.62 3.85
4226 7564 4.083643 GCAGAGACCGGTAAAGGTTTTAAC 60.084 45.833 7.34 0.00 46.09 2.01
4263 7601 7.131498 ACAACGTACTCTAAGTAACTCTCAG 57.869 40.000 0.00 0.00 31.62 3.35
4266 7604 5.352016 ACGTACTCTAAGTAACTCTCAGCTG 59.648 44.000 7.63 7.63 31.62 4.24
4271 7609 6.094881 ACTCTAAGTAACTCTCAGCTGCTAAG 59.905 42.308 9.47 8.50 0.00 2.18
4272 7610 6.181190 TCTAAGTAACTCTCAGCTGCTAAGA 58.819 40.000 9.47 0.99 0.00 2.10
4273 7611 4.981806 AGTAACTCTCAGCTGCTAAGAG 57.018 45.455 24.93 24.93 41.84 2.85
4274 7612 2.671130 AACTCTCAGCTGCTAAGAGC 57.329 50.000 26.15 0.00 40.15 4.09
4288 7626 4.625800 GAGCATCTCCAGCCGTTT 57.374 55.556 0.00 0.00 0.00 3.60
4289 7627 2.093216 GAGCATCTCCAGCCGTTTG 58.907 57.895 0.00 0.00 0.00 2.93
4290 7628 1.372087 GAGCATCTCCAGCCGTTTGG 61.372 60.000 0.00 0.00 39.70 3.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 6.333416 TGGAAATCTTAGTGAGTCGAGATTG 58.667 40.000 9.97 0.00 38.48 2.67
9 10 6.531503 TGGAAATCTTAGTGAGTCGAGATT 57.468 37.500 0.00 5.52 39.75 2.40
25 26 6.423001 GCAAATTATCTGATTGGCTGGAAATC 59.577 38.462 0.00 0.00 33.93 2.17
41 42 5.312079 AGAGCCAGACCTATGCAAATTATC 58.688 41.667 0.00 0.00 0.00 1.75
49 50 4.342665 ACTTAACTAGAGCCAGACCTATGC 59.657 45.833 0.00 0.00 0.00 3.14
117 118 1.740718 GCTGGAAATGAGACCGAGTCC 60.741 57.143 1.06 0.00 32.18 3.85
171 172 4.042062 TCCCTAGCCCTCAACATATTGATG 59.958 45.833 0.00 0.00 43.92 3.07
201 213 0.456221 TAGCCAGCTAGCGTCTGTTC 59.544 55.000 9.55 0.00 38.01 3.18
212 224 1.280133 TGAGAGCAACATTAGCCAGCT 59.720 47.619 0.00 0.00 38.43 4.24
226 238 0.813821 GCCAAATCCCTGTTGAGAGC 59.186 55.000 0.00 0.00 0.00 4.09
229 241 1.631405 TTGGCCAAATCCCTGTTGAG 58.369 50.000 17.98 0.00 0.00 3.02
253 265 3.120442 CGAGGTTGGGTGATTTTTCGTAC 60.120 47.826 0.00 0.00 0.00 3.67
300 312 6.259387 GGTTTAATATCCCAACGACGAAAGAT 59.741 38.462 0.00 0.88 0.00 2.40
345 357 5.749109 CGGATAGCTACATTCGAGACTTTTT 59.251 40.000 0.00 0.00 0.00 1.94
346 358 5.067413 TCGGATAGCTACATTCGAGACTTTT 59.933 40.000 0.00 0.00 30.94 2.27
347 359 4.579340 TCGGATAGCTACATTCGAGACTTT 59.421 41.667 0.00 0.00 30.94 2.66
348 360 4.135306 TCGGATAGCTACATTCGAGACTT 58.865 43.478 0.00 0.00 30.94 3.01
349 361 3.741249 TCGGATAGCTACATTCGAGACT 58.259 45.455 0.00 0.00 30.94 3.24
350 362 4.485024 TTCGGATAGCTACATTCGAGAC 57.515 45.455 0.00 0.00 37.24 3.36
351 363 4.760204 TCATTCGGATAGCTACATTCGAGA 59.240 41.667 0.00 0.00 37.24 4.04
352 364 4.854291 GTCATTCGGATAGCTACATTCGAG 59.146 45.833 0.00 0.00 37.24 4.04
353 365 4.519350 AGTCATTCGGATAGCTACATTCGA 59.481 41.667 0.00 0.00 34.11 3.71
354 366 4.799678 AGTCATTCGGATAGCTACATTCG 58.200 43.478 0.00 0.00 0.00 3.34
355 367 4.854291 CGAGTCATTCGGATAGCTACATTC 59.146 45.833 0.00 0.00 45.54 2.67
356 368 4.799678 CGAGTCATTCGGATAGCTACATT 58.200 43.478 0.00 0.00 45.54 2.71
357 369 4.427096 CGAGTCATTCGGATAGCTACAT 57.573 45.455 0.00 0.00 45.54 2.29
358 370 3.898517 CGAGTCATTCGGATAGCTACA 57.101 47.619 0.00 0.00 45.54 2.74
377 434 2.430942 GCAGCTTCGCAAATGCACG 61.431 57.895 6.18 0.00 42.21 5.34
392 449 5.349543 GCAAATTTTGTCATTTCCTAGGCAG 59.650 40.000 2.96 0.00 0.00 4.85
508 567 2.125106 CTAAGGTGTGCGAGGCCC 60.125 66.667 0.00 0.00 0.00 5.80
515 574 0.734942 TCGCTAACGCTAAGGTGTGC 60.735 55.000 0.00 0.00 39.84 4.57
547 606 1.759994 CGCTACGATGCAGGAGTAAG 58.240 55.000 0.00 0.00 0.00 2.34
587 657 3.802685 CGCTACAGTTACCTAATTCCAGC 59.197 47.826 0.00 0.00 0.00 4.85
678 751 1.770085 GCCGAGATTAGCAGCAGCAC 61.770 60.000 3.17 0.00 45.49 4.40
809 882 1.377229 CTTGAACCCCGGCCAGTAA 59.623 57.895 2.24 0.00 0.00 2.24
854 933 4.761058 AGGAGAAGCCGCGGGAGA 62.761 66.667 29.38 0.00 43.43 3.71
881 963 1.586154 CCTCGAAAATGCCGGCACTT 61.586 55.000 35.50 27.27 0.00 3.16
891 973 4.425520 GAGATCTTGACGACCTCGAAAAT 58.574 43.478 0.00 0.00 43.02 1.82
893 975 2.163815 GGAGATCTTGACGACCTCGAAA 59.836 50.000 0.00 0.00 43.02 3.46
934 1016 0.107993 CAGTCCGTGGCTGATGATGT 60.108 55.000 0.00 0.00 36.12 3.06
998 1092 1.553706 TGCTCTCAGTCTCAGCATCA 58.446 50.000 0.00 0.00 38.25 3.07
1001 1095 0.455005 CGATGCTCTCAGTCTCAGCA 59.545 55.000 0.00 0.00 46.87 4.41
1032 1126 1.603455 GGTGCAGCAAGTAGGGCAA 60.603 57.895 11.86 0.00 38.10 4.52
1047 1141 4.717233 TGAAATCATTTGAATCCGGGTG 57.283 40.909 0.00 0.00 0.00 4.61
1143 1246 2.200337 ACCAAAAGCCGGGCAGAAC 61.200 57.895 23.09 0.00 0.00 3.01
1152 1255 0.318120 CACCACCATCACCAAAAGCC 59.682 55.000 0.00 0.00 0.00 4.35
1155 1258 1.459455 CGCCACCACCATCACCAAAA 61.459 55.000 0.00 0.00 0.00 2.44
1167 1270 1.058284 AAAGTAGGTTACCGCCACCA 58.942 50.000 0.00 0.00 36.67 4.17
1175 1278 5.963214 TCCCCCAGAATAAAGTAGGTTAC 57.037 43.478 0.00 0.00 0.00 2.50
1178 1281 5.871324 TTTTCCCCCAGAATAAAGTAGGT 57.129 39.130 0.00 0.00 33.44 3.08
1183 1286 6.813293 ATTGGATTTTCCCCCAGAATAAAG 57.187 37.500 0.00 0.00 35.03 1.85
1189 1292 3.052944 CAGGTATTGGATTTTCCCCCAGA 60.053 47.826 0.00 0.00 35.03 3.86
1190 1293 3.299503 CAGGTATTGGATTTTCCCCCAG 58.700 50.000 0.00 0.00 35.03 4.45
1191 1294 2.625617 GCAGGTATTGGATTTTCCCCCA 60.626 50.000 0.00 0.00 35.03 4.96
1200 1303 3.745480 CGATGTTGGAGCAGGTATTGGAT 60.745 47.826 0.00 0.00 0.00 3.41
1206 1309 1.220749 GCCGATGTTGGAGCAGGTA 59.779 57.895 0.00 0.00 0.00 3.08
1207 1310 2.045926 GCCGATGTTGGAGCAGGT 60.046 61.111 0.00 0.00 0.00 4.00
1415 1531 3.898509 CCCTGAGCCGCGAGAGAG 61.899 72.222 8.23 0.00 0.00 3.20
1503 1643 4.379243 CTCCGGGCTGCGTGTTCT 62.379 66.667 0.00 0.00 0.00 3.01
1524 1668 2.749044 CTGTGGGCGCTCTTGCAT 60.749 61.111 9.62 0.00 39.64 3.96
1564 1708 7.168972 CGAATAGCCTCTGACTTGATCTTTAAG 59.831 40.741 0.00 0.00 0.00 1.85
1732 2014 6.621316 ACAAAAATAACCACGTGACACATA 57.379 33.333 19.30 2.75 0.00 2.29
1741 2023 3.969981 GTCCACGAACAAAAATAACCACG 59.030 43.478 0.00 0.00 0.00 4.94
1742 2024 4.922719 TGTCCACGAACAAAAATAACCAC 58.077 39.130 0.00 0.00 0.00 4.16
1743 2025 5.776173 ATGTCCACGAACAAAAATAACCA 57.224 34.783 0.00 0.00 31.81 3.67
1755 2037 7.519032 TGATATCTGTGTATATGTCCACGAA 57.481 36.000 3.98 0.00 34.28 3.85
1769 2051 5.045872 TGATCGCACTCTTTGATATCTGTG 58.954 41.667 3.98 6.64 0.00 3.66
1862 2144 0.449786 TGTAATTGCCATGCGTTCCG 59.550 50.000 0.00 0.00 0.00 4.30
1934 2238 2.158505 ACTAGTAATCGGCAGGCTAGGA 60.159 50.000 0.00 0.00 34.94 2.94
2054 4857 7.486647 AGCTATTATGACCTGAAAAGCAATTG 58.513 34.615 0.00 0.00 0.00 2.32
2098 4915 4.208686 GGCCACTAGCGACCGAGG 62.209 72.222 0.00 0.00 45.17 4.63
2206 5023 1.600023 TAGTTGGCCACGGTTTTGAG 58.400 50.000 3.88 0.00 0.00 3.02
2265 5082 5.193663 TCTTCTAAAGAGATGAGCATCCG 57.806 43.478 6.84 0.00 38.58 4.18
2289 5107 7.001674 TCAAAATTGTTGGTAGCCTTCTCTAA 58.998 34.615 0.00 0.00 0.00 2.10
2330 5148 2.606587 GCCATGTCCACCTCCACCT 61.607 63.158 0.00 0.00 0.00 4.00
2342 5160 2.553028 CCCTTTGTAGACAGTGCCATGT 60.553 50.000 0.00 0.00 35.68 3.21
2508 5327 0.110192 GCAAGTAACGGCACTTCTGC 60.110 55.000 1.32 1.26 43.41 4.26
2519 5338 6.073440 TGGAAATGAACTCGTAAGCAAGTAAC 60.073 38.462 0.00 0.00 37.18 2.50
2571 5390 2.687805 GCGACCCTCCTTTTTCCGC 61.688 63.158 0.00 0.00 0.00 5.54
2585 5404 3.132467 ACCTATCTTTCCAAGGTAGCGAC 59.868 47.826 0.00 0.00 41.86 5.19
2780 5605 2.020720 CCTTGCACCACAGTTGTTGTA 58.979 47.619 0.00 0.00 38.16 2.41
2791 5616 2.557869 ACCCTATAGTTCCTTGCACCA 58.442 47.619 0.00 0.00 0.00 4.17
2849 5674 8.116753 CCAAAGCTATAAACATCACTACTTTCG 58.883 37.037 0.00 0.00 0.00 3.46
2894 5719 4.078863 AGAGATGGCTTCCTCCTAGTAAGT 60.079 45.833 0.00 0.00 0.00 2.24
2994 5820 6.078664 CCTCCTCTATAACTTGTGGGTCTAT 58.921 44.000 0.00 0.00 0.00 1.98
3028 5854 6.942886 CTAGAGTAGCAACTTCTTTCACTG 57.057 41.667 0.00 0.00 35.56 3.66
3147 5973 4.949856 TGTTTCTTCTATCAAATCAGCCCC 59.050 41.667 0.00 0.00 0.00 5.80
3299 6213 6.128822 GGCTAAAAATTCACTTACAAGCAAGC 60.129 38.462 0.00 0.00 0.00 4.01
3508 6448 4.021104 TGGATAGTGTCTTGGTCAGTCTTG 60.021 45.833 0.00 0.00 0.00 3.02
3586 6526 5.337578 ACTACCACAAGTTGCACAATTTT 57.662 34.783 1.81 0.00 0.00 1.82
3848 6800 4.762765 ACGCTCGAATCATAGAGGTTCTAT 59.237 41.667 0.00 0.00 40.13 1.98
3849 6801 4.023963 CACGCTCGAATCATAGAGGTTCTA 60.024 45.833 0.00 0.00 35.19 2.10
3877 6829 0.107800 CTCATCACCAGTCCCTGCTG 60.108 60.000 0.00 0.00 36.31 4.41
3942 6894 0.534652 CTGCTGGGAGCCTCAATAGC 60.535 60.000 7.02 7.02 41.51 2.97
3945 6897 2.146146 TTGCTGCTGGGAGCCTCAAT 62.146 55.000 11.30 0.00 41.51 2.57
3971 6923 3.576982 ACACCCATAGAAACTTGACTCGA 59.423 43.478 0.00 0.00 0.00 4.04
3986 6938 2.376518 ACAGGTCAATGAGAACACCCAT 59.623 45.455 0.00 0.00 35.97 4.00
3988 6940 2.427506 GACAGGTCAATGAGAACACCC 58.572 52.381 0.00 0.00 35.97 4.61
4025 6977 6.860023 GGTTATATTGCACGGTAGTAGTACAG 59.140 42.308 9.89 8.08 0.00 2.74
4089 7041 6.325804 GGGTAGTTAGAAGGGCAATTAGAGTA 59.674 42.308 0.00 0.00 0.00 2.59
4092 7044 5.130477 CAGGGTAGTTAGAAGGGCAATTAGA 59.870 44.000 0.00 0.00 0.00 2.10
4093 7045 5.104485 ACAGGGTAGTTAGAAGGGCAATTAG 60.104 44.000 0.00 0.00 0.00 1.73
4094 7046 4.786454 ACAGGGTAGTTAGAAGGGCAATTA 59.214 41.667 0.00 0.00 0.00 1.40
4095 7047 3.591977 ACAGGGTAGTTAGAAGGGCAATT 59.408 43.478 0.00 0.00 0.00 2.32
4096 7048 3.190439 ACAGGGTAGTTAGAAGGGCAAT 58.810 45.455 0.00 0.00 0.00 3.56
4097 7049 2.627933 ACAGGGTAGTTAGAAGGGCAA 58.372 47.619 0.00 0.00 0.00 4.52
4098 7050 2.337359 ACAGGGTAGTTAGAAGGGCA 57.663 50.000 0.00 0.00 0.00 5.36
4099 7051 5.366460 GAATTACAGGGTAGTTAGAAGGGC 58.634 45.833 0.00 0.00 0.00 5.19
4100 7052 5.163227 GGGAATTACAGGGTAGTTAGAAGGG 60.163 48.000 0.00 0.00 0.00 3.95
4101 7053 5.163227 GGGGAATTACAGGGTAGTTAGAAGG 60.163 48.000 0.00 0.00 0.00 3.46
4119 7457 1.062962 CATGGGGCTTTACAGGGGAAT 60.063 52.381 0.00 0.00 0.00 3.01
4120 7458 0.334676 CATGGGGCTTTACAGGGGAA 59.665 55.000 0.00 0.00 0.00 3.97
4121 7459 0.849094 ACATGGGGCTTTACAGGGGA 60.849 55.000 0.00 0.00 0.00 4.81
4122 7460 0.684153 CACATGGGGCTTTACAGGGG 60.684 60.000 0.00 0.00 0.00 4.79
4123 7461 0.039618 ACACATGGGGCTTTACAGGG 59.960 55.000 0.00 0.00 0.00 4.45
4124 7462 1.004745 AGACACATGGGGCTTTACAGG 59.995 52.381 0.00 0.00 0.00 4.00
4125 7463 2.496899 AGACACATGGGGCTTTACAG 57.503 50.000 0.00 0.00 0.00 2.74
4126 7464 2.355716 GCTAGACACATGGGGCTTTACA 60.356 50.000 9.70 0.00 0.00 2.41
4127 7465 2.289565 GCTAGACACATGGGGCTTTAC 58.710 52.381 9.70 0.00 0.00 2.01
4128 7466 1.912731 TGCTAGACACATGGGGCTTTA 59.087 47.619 9.70 0.00 0.00 1.85
4129 7467 0.698238 TGCTAGACACATGGGGCTTT 59.302 50.000 9.70 0.00 0.00 3.51
4130 7468 0.921896 ATGCTAGACACATGGGGCTT 59.078 50.000 9.70 0.00 0.00 4.35
4131 7469 0.921896 AATGCTAGACACATGGGGCT 59.078 50.000 9.22 9.22 0.00 5.19
4132 7470 1.027357 CAATGCTAGACACATGGGGC 58.973 55.000 0.00 0.00 0.00 5.80
4133 7471 1.027357 GCAATGCTAGACACATGGGG 58.973 55.000 0.00 0.00 0.00 4.96
4134 7472 1.945394 GAGCAATGCTAGACACATGGG 59.055 52.381 8.12 0.00 39.88 4.00
4135 7473 2.871022 GAGAGCAATGCTAGACACATGG 59.129 50.000 8.12 0.00 39.88 3.66
4136 7474 3.794717 AGAGAGCAATGCTAGACACATG 58.205 45.455 8.12 0.00 39.88 3.21
4137 7475 4.440880 GAAGAGAGCAATGCTAGACACAT 58.559 43.478 8.12 0.00 39.88 3.21
4193 7531 2.515523 GTCTCTGCATGGGCGCAT 60.516 61.111 11.00 11.00 45.35 4.73
4211 7549 6.656003 CAGTTGAGAGTTAAAACCTTTACCG 58.344 40.000 0.00 0.00 0.00 4.02
4226 7564 4.547532 AGTACGTTGTTAGCAGTTGAGAG 58.452 43.478 0.00 0.00 0.00 3.20
4266 7604 0.599728 CGGCTGGAGATGCTCTTAGC 60.600 60.000 12.47 12.47 42.82 3.09
4271 7609 1.372087 CCAAACGGCTGGAGATGCTC 61.372 60.000 0.00 0.00 38.96 4.26
4272 7610 1.377725 CCAAACGGCTGGAGATGCT 60.378 57.895 0.00 0.00 38.96 3.79
4273 7611 3.056313 GCCAAACGGCTGGAGATGC 62.056 63.158 9.09 0.00 46.85 3.91
4274 7612 3.190878 GCCAAACGGCTGGAGATG 58.809 61.111 9.09 0.00 46.85 2.90


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

AutoCloner maintained by Alex Coulton.