Multiple sequence alignment - TraesCS4B01G003700

Loading Multiple Alignment...

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 TraesCS4B01G003700 chr4B 100.000 3341 0 0 1 3341 2337432 2334092 0.000000e+00 6170
1 TraesCS4B01G003700 chr4D 95.019 1305 55 2 1 1302 1995158 1996455 0.000000e+00 2041
2 TraesCS4B01G003700 chr4D 93.970 1194 60 8 1310 2501 1996799 1997982 0.000000e+00 1796
3 TraesCS4B01G003700 chr5B 95.386 1192 55 0 1310 2501 14706191 14707382 0.000000e+00 1897
4 TraesCS4B01G003700 chr5B 93.735 846 39 2 2509 3341 410223579 410222735 0.000000e+00 1256
5 TraesCS4B01G003700 chr5B 95.532 761 16 2 2501 3243 528179464 528180224 0.000000e+00 1201
6 TraesCS4B01G003700 chr5B 84.263 1201 157 19 1311 2501 113676712 113675534 0.000000e+00 1142
7 TraesCS4B01G003700 chr5B 81.818 1287 196 23 29 1302 113683821 113682560 0.000000e+00 1046
8 TraesCS4B01G003700 chr5B 80.468 1239 206 20 78 1302 515184000 515185216 0.000000e+00 915
9 TraesCS4B01G003700 chr5B 94.397 589 18 5 2501 3076 391057180 391057766 0.000000e+00 891
10 TraesCS4B01G003700 chr5B 93.956 546 23 2 760 1302 14703731 14704269 0.000000e+00 817
11 TraesCS4B01G003700 chr5B 95.859 483 20 0 1 483 14703206 14703688 0.000000e+00 782
12 TraesCS4B01G003700 chr3B 94.028 854 37 2 2501 3341 807330724 807329872 0.000000e+00 1282
13 TraesCS4B01G003700 chr3B 83.292 1197 168 18 1311 2482 54786227 54787416 0.000000e+00 1074
14 TraesCS4B01G003700 chr3B 82.907 1211 174 20 1311 2495 54795783 54796986 0.000000e+00 1059
15 TraesCS4B01G003700 chr3B 81.077 1300 210 21 17 1298 54784645 54785926 0.000000e+00 1005
16 TraesCS4B01G003700 chr3B 79.892 1293 222 26 27 1302 54794140 54795411 0.000000e+00 913
17 TraesCS4B01G003700 chr3B 83.840 724 103 9 2625 3341 629549695 629548979 0.000000e+00 676
18 TraesCS4B01G003700 chr7B 93.794 854 39 3 2501 3341 537211037 537211889 0.000000e+00 1271
19 TraesCS4B01G003700 chr7B 93.450 855 37 4 2501 3341 593292323 593291474 0.000000e+00 1251
20 TraesCS4B01G003700 chr2A 93.443 854 36 3 2501 3341 762946528 762945682 0.000000e+00 1249
21 TraesCS4B01G003700 chr2B 92.857 854 47 2 2501 3341 707566908 707566056 0.000000e+00 1227
22 TraesCS4B01G003700 chr2B 87.298 866 79 15 2501 3339 18026217 18027078 0.000000e+00 961
23 TraesCS4B01G003700 chr2B 93.061 490 20 5 2501 2977 385888219 385887731 0.000000e+00 704
24 TraesCS4B01G003700 chr5D 84.430 1201 157 18 1311 2501 104256101 104254921 0.000000e+00 1155
25 TraesCS4B01G003700 chr5D 82.284 1287 188 22 29 1302 104257705 104256446 0.000000e+00 1077
26 TraesCS4B01G003700 chr5D 80.575 1148 195 14 164 1302 425838914 425840042 0.000000e+00 859
27 TraesCS4B01G003700 chr3A 82.181 1302 202 15 17 1300 44709652 44710941 0.000000e+00 1092
28 TraesCS4B01G003700 chr3A 83.039 1191 170 19 1311 2482 44711306 44712483 0.000000e+00 1051
29 TraesCS4B01G003700 chr3A 84.284 1069 150 12 1311 2364 44640985 44642050 0.000000e+00 1027
30 TraesCS4B01G003700 chr3A 79.491 1297 240 17 17 1302 44639332 44640613 0.000000e+00 898
31 TraesCS4B01G003700 chrUn 81.504 1303 211 16 16 1302 47549202 47547914 0.000000e+00 1044
32 TraesCS4B01G003700 chr3D 81.303 1305 208 20 17 1302 32278716 32280003 0.000000e+00 1026
33 TraesCS4B01G003700 chr3D 88.479 868 72 11 2501 3341 378565332 378566198 0.000000e+00 1024
34 TraesCS4B01G003700 chr3D 80.854 1311 216 19 17 1302 32299413 32300713 0.000000e+00 998
35 TraesCS4B01G003700 chr5A 80.786 1119 182 21 189 1297 540052000 540053095 0.000000e+00 845
36 TraesCS4B01G003700 chr6B 91.573 534 27 6 2501 3019 653771379 653770849 0.000000e+00 721
37 TraesCS4B01G003700 chr1B 87.500 160 19 1 1841 1999 679214746 679214587 2.050000e-42 183


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 TraesCS4B01G003700 chr4B 2334092 2337432 3340 True 6170.000000 6170 100.0000 1 3341 1 chr4B.!!$R1 3340
1 TraesCS4B01G003700 chr4D 1995158 1997982 2824 False 1918.500000 2041 94.4945 1 2501 2 chr4D.!!$F1 2500
2 TraesCS4B01G003700 chr5B 410222735 410223579 844 True 1256.000000 1256 93.7350 2509 3341 1 chr5B.!!$R3 832
3 TraesCS4B01G003700 chr5B 528179464 528180224 760 False 1201.000000 1201 95.5320 2501 3243 1 chr5B.!!$F3 742
4 TraesCS4B01G003700 chr5B 14703206 14707382 4176 False 1165.333333 1897 95.0670 1 2501 3 chr5B.!!$F4 2500
5 TraesCS4B01G003700 chr5B 113675534 113676712 1178 True 1142.000000 1142 84.2630 1311 2501 1 chr5B.!!$R1 1190
6 TraesCS4B01G003700 chr5B 113682560 113683821 1261 True 1046.000000 1046 81.8180 29 1302 1 chr5B.!!$R2 1273
7 TraesCS4B01G003700 chr5B 515184000 515185216 1216 False 915.000000 915 80.4680 78 1302 1 chr5B.!!$F2 1224
8 TraesCS4B01G003700 chr5B 391057180 391057766 586 False 891.000000 891 94.3970 2501 3076 1 chr5B.!!$F1 575
9 TraesCS4B01G003700 chr3B 807329872 807330724 852 True 1282.000000 1282 94.0280 2501 3341 1 chr3B.!!$R2 840
10 TraesCS4B01G003700 chr3B 54784645 54787416 2771 False 1039.500000 1074 82.1845 17 2482 2 chr3B.!!$F1 2465
11 TraesCS4B01G003700 chr3B 54794140 54796986 2846 False 986.000000 1059 81.3995 27 2495 2 chr3B.!!$F2 2468
12 TraesCS4B01G003700 chr3B 629548979 629549695 716 True 676.000000 676 83.8400 2625 3341 1 chr3B.!!$R1 716
13 TraesCS4B01G003700 chr7B 537211037 537211889 852 False 1271.000000 1271 93.7940 2501 3341 1 chr7B.!!$F1 840
14 TraesCS4B01G003700 chr7B 593291474 593292323 849 True 1251.000000 1251 93.4500 2501 3341 1 chr7B.!!$R1 840
15 TraesCS4B01G003700 chr2A 762945682 762946528 846 True 1249.000000 1249 93.4430 2501 3341 1 chr2A.!!$R1 840
16 TraesCS4B01G003700 chr2B 707566056 707566908 852 True 1227.000000 1227 92.8570 2501 3341 1 chr2B.!!$R2 840
17 TraesCS4B01G003700 chr2B 18026217 18027078 861 False 961.000000 961 87.2980 2501 3339 1 chr2B.!!$F1 838
18 TraesCS4B01G003700 chr5D 104254921 104257705 2784 True 1116.000000 1155 83.3570 29 2501 2 chr5D.!!$R1 2472
19 TraesCS4B01G003700 chr5D 425838914 425840042 1128 False 859.000000 859 80.5750 164 1302 1 chr5D.!!$F1 1138
20 TraesCS4B01G003700 chr3A 44709652 44712483 2831 False 1071.500000 1092 82.6100 17 2482 2 chr3A.!!$F2 2465
21 TraesCS4B01G003700 chr3A 44639332 44642050 2718 False 962.500000 1027 81.8875 17 2364 2 chr3A.!!$F1 2347
22 TraesCS4B01G003700 chrUn 47547914 47549202 1288 True 1044.000000 1044 81.5040 16 1302 1 chrUn.!!$R1 1286
23 TraesCS4B01G003700 chr3D 32278716 32280003 1287 False 1026.000000 1026 81.3030 17 1302 1 chr3D.!!$F1 1285
24 TraesCS4B01G003700 chr3D 378565332 378566198 866 False 1024.000000 1024 88.4790 2501 3341 1 chr3D.!!$F3 840
25 TraesCS4B01G003700 chr3D 32299413 32300713 1300 False 998.000000 998 80.8540 17 1302 1 chr3D.!!$F2 1285
26 TraesCS4B01G003700 chr5A 540052000 540053095 1095 False 845.000000 845 80.7860 189 1297 1 chr5A.!!$F1 1108
27 TraesCS4B01G003700 chr6B 653770849 653771379 530 True 721.000000 721 91.5730 2501 3019 1 chr6B.!!$R1 518

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
576 624 0.443869 CGATGCCTTCTTTGGTGTCG 59.556 55.000 0.00 0.0 32.96 4.35 F
854 905 1.270839 GCTAACACAGGCTTCCAGACA 60.271 52.381 0.00 0.0 0.00 3.41 F
1421 3425 0.524816 CGTAATGTCTACAGCGGCGT 60.525 55.000 9.37 0.0 0.00 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1402 3406 0.524816 ACGCCGCTGTAGACATTACG 60.525 55.0 0.0 0.0 0.0 3.18 R
1659 3663 0.529337 CGATGCAGATCTCAAGGCGT 60.529 55.0 0.0 0.0 0.0 5.68 R
3280 5395 0.977627 TCCGATGTGCCTGACTCCAT 60.978 55.0 0.0 0.0 0.0 3.41 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
72 80 7.436118 TCTTCCAATTTTCCTGACATTTTCTG 58.564 34.615 0.00 0.00 0.00 3.02
153 177 5.468072 AGACATCTTGTAGCAAACAGAAGTG 59.532 40.000 0.00 0.00 39.87 3.16
335 377 4.515191 TCAAACCAAGACAATGACAGTAGC 59.485 41.667 0.00 0.00 0.00 3.58
356 398 3.546009 CGTATGTGGGACGGGGAT 58.454 61.111 0.00 0.00 36.66 3.85
383 425 3.876914 GCTCCAAATTCATGACATCGGTA 59.123 43.478 0.00 0.00 0.00 4.02
576 624 0.443869 CGATGCCTTCTTTGGTGTCG 59.556 55.000 0.00 0.00 32.96 4.35
599 647 4.821940 CCTTAGGGAATCTAGTCCTCCTT 58.178 47.826 0.00 0.00 37.85 3.36
741 792 6.072508 TCAGAACAGTTCTTATGCATTTGTCC 60.073 38.462 13.53 0.00 38.11 4.02
786 837 4.024556 CACCTGACATCTTCACAACAGTTC 60.025 45.833 0.00 0.00 0.00 3.01
854 905 1.270839 GCTAACACAGGCTTCCAGACA 60.271 52.381 0.00 0.00 0.00 3.41
978 1041 2.987232 GGGTGACATACTCCAAACTCC 58.013 52.381 0.00 0.00 34.21 3.85
979 1042 2.304761 GGGTGACATACTCCAAACTCCA 59.695 50.000 0.00 0.00 34.21 3.86
1086 1149 3.827505 ACCAACTGCACAGGTCAAT 57.172 47.368 2.21 0.00 0.00 2.57
1122 1185 6.433093 ACCTTACATGGATTTTACCTGTTGAC 59.567 38.462 0.00 0.00 0.00 3.18
1239 1302 1.902918 GACAGCACAATGGGCCACA 60.903 57.895 9.28 0.00 0.00 4.17
1279 1342 2.099427 GGAGGACTCGGTAGAACATCAC 59.901 54.545 0.00 0.00 0.00 3.06
1290 1353 6.482641 TCGGTAGAACATCACATAGAGACTAC 59.517 42.308 0.00 0.00 0.00 2.73
1302 1365 5.535030 ACATAGAGACTACGTTATCATGGCA 59.465 40.000 0.00 0.00 0.00 4.92
1305 1368 5.533482 AGAGACTACGTTATCATGGCAATC 58.467 41.667 0.00 0.00 0.00 2.67
1306 1369 4.632153 AGACTACGTTATCATGGCAATCC 58.368 43.478 0.00 0.00 0.00 3.01
1402 3406 2.726821 TCATTGGCAGAGGTGGATTTC 58.273 47.619 0.00 0.00 0.00 2.17
1421 3425 0.524816 CGTAATGTCTACAGCGGCGT 60.525 55.000 9.37 0.00 0.00 5.68
1479 3483 1.158007 ACCAGGAATCCCAACAAGGT 58.842 50.000 0.00 0.00 34.66 3.50
1481 3485 2.719705 ACCAGGAATCCCAACAAGGTTA 59.280 45.455 0.00 0.00 34.66 2.85
1517 3521 5.048921 AGACTGAAATTGAGATGTTGTGCAG 60.049 40.000 0.00 0.00 0.00 4.41
1520 3524 5.283294 TGAAATTGAGATGTTGTGCAGTTG 58.717 37.500 0.00 0.00 0.00 3.16
1581 3585 6.687393 GCCAGGACAAGAATGAGATGATTCTA 60.687 42.308 0.00 0.00 41.02 2.10
1611 3615 8.803204 ATGACTACATGGCTCATGGAACACTC 62.803 46.154 16.39 4.59 45.16 3.51
1638 3642 4.460263 AGCATCTGTACAACACCAGAAAA 58.540 39.130 0.00 0.00 40.81 2.29
1642 3646 4.196193 TCTGTACAACACCAGAAAACCAG 58.804 43.478 0.00 0.00 34.88 4.00
1648 3652 1.064758 ACACCAGAAAACCAGCACTGA 60.065 47.619 0.00 0.00 32.90 3.41
1659 3663 3.279116 GCACTGACGTGGCAGCAA 61.279 61.111 1.75 0.00 41.51 3.91
1953 3957 5.624509 CGGAGTCATGTTGTTTGAGATCCTA 60.625 44.000 0.00 0.00 32.03 2.94
2295 4329 3.871594 ACTCAATAATTAGTGTCGCTGCC 59.128 43.478 12.28 0.00 0.00 4.85
2306 4340 3.847602 CGCTGCCCAGGGAGAGAG 61.848 72.222 10.89 1.50 43.22 3.20
2393 4434 6.488683 TGAAAGGTTCATTGTTACCTAACTGG 59.511 38.462 11.74 0.00 43.88 4.00
2631 4729 4.618489 CGGAGCAAAATAAAGCACAAAGAG 59.382 41.667 0.00 0.00 0.00 2.85
2632 4730 5.562696 CGGAGCAAAATAAAGCACAAAGAGA 60.563 40.000 0.00 0.00 0.00 3.10
2793 4894 0.108756 GGAGTGAGTAAGGACCACGC 60.109 60.000 0.00 0.00 34.07 5.34
2811 4912 0.108138 GCACGGATCCAAGCTGTAGT 60.108 55.000 13.41 0.00 0.00 2.73
2949 5063 1.156736 CAGCTAACCACGTCCCAAAG 58.843 55.000 0.00 0.00 0.00 2.77
2963 5077 4.142687 CGTCCCAAAGAAAGACGCAATATT 60.143 41.667 0.00 0.00 45.72 1.28
3128 5243 9.654663 GAGTAAGTTGTCCTTTGTGAGTATTAT 57.345 33.333 0.00 0.00 34.46 1.28
3321 5436 5.872070 GGAGAGTCGAACTTCAATCAATCTT 59.128 40.000 0.00 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 80 5.675684 TTTTCTTTATGGGATTTGGAGCC 57.324 39.130 0.00 0.00 0.00 4.70
233 266 2.673368 GGCAATCGACAAGAGTACCAAG 59.327 50.000 0.00 0.00 0.00 3.61
356 398 2.026729 TGTCATGAATTTGGAGCCGGTA 60.027 45.455 1.90 0.00 0.00 4.02
576 624 2.901192 GGAGGACTAGATTCCCTAAGGC 59.099 54.545 0.00 0.00 36.12 4.35
599 647 6.314018 CGTTTGTGAAGCATTGAAGCTATTA 58.686 36.000 0.00 0.00 45.89 0.98
635 683 5.428253 TCACAGACAAGGTAGGCATAATTC 58.572 41.667 0.00 0.00 0.00 2.17
786 837 5.641783 TCATGGTGGACAAATATTGTGTG 57.358 39.130 0.00 0.00 45.52 3.82
854 905 2.352388 CCGACATTGAACCGGTACATT 58.648 47.619 8.00 0.00 38.55 2.71
1086 1149 6.620877 ATCCATGTAAGGTTGTAGTTCAGA 57.379 37.500 0.00 0.00 0.00 3.27
1122 1185 1.093496 GGAGGTAAATGAACCCCGCG 61.093 60.000 0.00 0.00 40.71 6.46
1239 1302 4.202202 CCTCCGCTCAAAGAGATTACATCT 60.202 45.833 0.00 0.00 43.70 2.90
1279 1342 6.013842 TGCCATGATAACGTAGTCTCTATG 57.986 41.667 0.00 0.00 45.00 2.23
1302 1365 2.876550 CACGAGATCACATGCATGGATT 59.123 45.455 29.41 13.76 0.00 3.01
1305 1368 0.306840 GCACGAGATCACATGCATGG 59.693 55.000 29.41 18.30 38.00 3.66
1306 1369 0.042448 CGCACGAGATCACATGCATG 60.042 55.000 25.09 25.09 37.97 4.06
1307 1370 0.460811 ACGCACGAGATCACATGCAT 60.461 50.000 11.58 0.00 37.97 3.96
1402 3406 0.524816 ACGCCGCTGTAGACATTACG 60.525 55.000 0.00 0.00 0.00 3.18
1421 3425 3.455910 CACCTTTGTCCCTCCATCTATCA 59.544 47.826 0.00 0.00 0.00 2.15
1479 3483 8.102676 TCAATTTCAGTCTGGAACTCATGATAA 58.897 33.333 0.00 0.00 35.45 1.75
1481 3485 6.479006 TCAATTTCAGTCTGGAACTCATGAT 58.521 36.000 0.00 0.00 35.45 2.45
1533 3537 5.586243 GCAGTAGCCAATCAAAGATACAAGA 59.414 40.000 0.00 0.00 33.58 3.02
1581 3585 4.202295 CCATGAGCCATGTAGTCATACACT 60.202 45.833 12.36 0.00 44.51 3.55
1611 3615 1.726791 GTGTTGTACAGATGCTCACGG 59.273 52.381 0.00 0.00 0.00 4.94
1638 3642 3.814615 CTGCCACGTCAGTGCTGGT 62.815 63.158 0.00 0.00 46.62 4.00
1642 3646 3.279116 TTGCTGCCACGTCAGTGC 61.279 61.111 6.18 0.40 46.62 4.40
1659 3663 0.529337 CGATGCAGATCTCAAGGCGT 60.529 55.000 0.00 0.00 0.00 5.68
1728 3732 3.857052 TGTCTTAACATCACGGTGGATC 58.143 45.455 8.50 0.00 0.00 3.36
1860 3864 7.518188 AGTACTCCGGATCAAAATATCCAAAT 58.482 34.615 3.57 0.00 44.98 2.32
1953 3957 2.867793 TTATCACAGGGCGCGCACAT 62.868 55.000 37.52 22.55 0.00 3.21
2184 4188 1.968540 GTCCTGCAACCTGAGTGCC 60.969 63.158 0.00 0.00 0.00 5.01
2295 4329 6.684897 ATATCTGAAAATCTCTCTCCCTGG 57.315 41.667 0.00 0.00 0.00 4.45
2444 4491 5.546499 TGAGAGTTTTATACCAAGGTCACCT 59.454 40.000 0.00 0.00 33.87 4.00
2793 4894 2.093973 AGAACTACAGCTTGGATCCGTG 60.094 50.000 7.39 3.21 0.00 4.94
2949 5063 7.259290 TCCTCCAATAAATATTGCGTCTTTC 57.741 36.000 7.50 0.00 41.23 2.62
3191 5306 1.918800 CCTGTCCCGAGGTCCCTTT 60.919 63.158 0.00 0.00 0.00 3.11
3280 5395 0.977627 TCCGATGTGCCTGACTCCAT 60.978 55.000 0.00 0.00 0.00 3.41
3321 5436 2.028420 CCTGGATGCACTTGATTCGA 57.972 50.000 0.00 0.00 0.00 3.71


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

AutoCloner maintained by Alex Coulton.