Multiple sequence alignment - TraesCS4D01G067700

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 TraesCS4D01G067700 chr4D 100.000 4401 0 0 617 5017 43068568 43072968 0.000000e+00 8128
1 TraesCS4D01G067700 chr4D 100.000 232 0 0 1 232 43067952 43068183 3.590000e-116 429
2 TraesCS4D01G067700 chr4B 93.019 4226 165 44 617 4770 61309940 61314107 0.000000e+00 6050
3 TraesCS4D01G067700 chr4B 93.805 2712 102 30 2347 5017 140423712 140426398 0.000000e+00 4017
4 TraesCS4D01G067700 chr4B 91.605 1751 73 28 3298 5017 62041368 62043075 0.000000e+00 2351
5 TraesCS4D01G067700 chr4B 92.727 1650 73 14 3409 5017 140210987 140212630 0.000000e+00 2338
6 TraesCS4D01G067700 chr4B 96.603 942 23 5 2347 3284 140201812 140202748 0.000000e+00 1554
7 TraesCS4D01G067700 chr4B 91.495 1070 52 20 3953 5014 62858626 62859664 0.000000e+00 1435
8 TraesCS4D01G067700 chr4B 91.146 1073 55 21 3953 5017 61546607 61545567 0.000000e+00 1419
9 TraesCS4D01G067700 chr4B 91.735 859 48 8 4177 5017 140431935 140432788 0.000000e+00 1171
10 TraesCS4D01G067700 chr4B 92.143 840 43 9 4199 5017 62417196 62418033 0.000000e+00 1164
11 TraesCS4D01G067700 chr4B 91.579 855 47 7 4177 5017 140218194 140219037 0.000000e+00 1157
12 TraesCS4D01G067700 chr4B 92.174 805 26 6 3301 4087 61534293 61533508 0.000000e+00 1103
13 TraesCS4D01G067700 chr4B 93.995 383 21 2 3301 3682 61887846 61887465 3.370000e-161 579
14 TraesCS4D01G067700 chr4B 94.556 349 16 3 3546 3892 61490473 61490820 2.060000e-148 536
15 TraesCS4D01G067700 chr4B 93.315 359 23 1 3558 3915 62109558 62109916 3.440000e-146 529
16 TraesCS4D01G067700 chr4B 88.770 374 21 10 3298 3671 62436964 62437316 5.960000e-119 438
17 TraesCS4D01G067700 chr4B 94.946 277 13 1 2234 2510 140201536 140201811 2.770000e-117 433
18 TraesCS4D01G067700 chr4B 92.953 298 13 4 3912 4201 61490877 61491174 1.290000e-115 427
19 TraesCS4D01G067700 chr4B 95.489 266 11 1 3298 3562 62058347 62058612 1.670000e-114 424
20 TraesCS4D01G067700 chr4B 93.863 277 16 1 2234 2510 140423436 140423711 2.790000e-112 416
21 TraesCS4D01G067700 chr4B 87.433 374 22 11 3298 3671 62435305 62435653 1.680000e-109 407
22 TraesCS4D01G067700 chr4B 93.939 264 15 1 4754 5017 61532736 61532474 1.010000e-106 398
23 TraesCS4D01G067700 chr4B 91.373 255 16 4 4767 5017 61314272 61314524 1.340000e-90 344
24 TraesCS4D01G067700 chr4B 92.766 235 13 3 1 232 61309636 61309869 2.240000e-88 337
25 TraesCS4D01G067700 chr4B 86.891 267 12 6 3945 4205 62399063 62399312 1.380000e-70 278
26 TraesCS4D01G067700 chr4A 93.252 4031 153 42 617 4550 556826318 556822310 0.000000e+00 5827
27 TraesCS4D01G067700 chr4A 89.032 465 41 10 4556 5013 556821948 556821487 7.290000e-158 568
28 TraesCS4D01G067700 chr4A 94.894 235 9 1 1 232 556826621 556826387 1.030000e-96 364
29 TraesCS4D01G067700 chr1D 93.542 480 22 6 3980 4452 55619489 55619012 0.000000e+00 706
30 TraesCS4D01G067700 chr1D 91.768 413 28 3 4606 5017 55616247 55615840 2.030000e-158 569


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 TraesCS4D01G067700 chr4D 43067952 43072968 5016 False 4278.500000 8128 100.000000 1 5017 2 chr4D.!!$F1 5016
1 TraesCS4D01G067700 chr4B 62041368 62043075 1707 False 2351.000000 2351 91.605000 3298 5017 1 chr4B.!!$F1 1719
2 TraesCS4D01G067700 chr4B 140210987 140212630 1643 False 2338.000000 2338 92.727000 3409 5017 1 chr4B.!!$F7 1608
3 TraesCS4D01G067700 chr4B 61309636 61314524 4888 False 2243.666667 6050 92.386000 1 5017 3 chr4B.!!$F10 5016
4 TraesCS4D01G067700 chr4B 140423436 140426398 2962 False 2216.500000 4017 93.834000 2234 5017 2 chr4B.!!$F14 2783
5 TraesCS4D01G067700 chr4B 62858626 62859664 1038 False 1435.000000 1435 91.495000 3953 5014 1 chr4B.!!$F6 1061
6 TraesCS4D01G067700 chr4B 61545567 61546607 1040 True 1419.000000 1419 91.146000 3953 5017 1 chr4B.!!$R1 1064
7 TraesCS4D01G067700 chr4B 140431935 140432788 853 False 1171.000000 1171 91.735000 4177 5017 1 chr4B.!!$F9 840
8 TraesCS4D01G067700 chr4B 62417196 62418033 837 False 1164.000000 1164 92.143000 4199 5017 1 chr4B.!!$F5 818
9 TraesCS4D01G067700 chr4B 140218194 140219037 843 False 1157.000000 1157 91.579000 4177 5017 1 chr4B.!!$F8 840
10 TraesCS4D01G067700 chr4B 140201536 140202748 1212 False 993.500000 1554 95.774500 2234 3284 2 chr4B.!!$F13 1050
11 TraesCS4D01G067700 chr4B 61532474 61534293 1819 True 750.500000 1103 93.056500 3301 5017 2 chr4B.!!$R3 1716
12 TraesCS4D01G067700 chr4B 61490473 61491174 701 False 481.500000 536 93.754500 3546 4201 2 chr4B.!!$F11 655
13 TraesCS4D01G067700 chr4B 62435305 62437316 2011 False 422.500000 438 88.101500 3298 3671 2 chr4B.!!$F12 373
14 TraesCS4D01G067700 chr4A 556821487 556826621 5134 True 2253.000000 5827 92.392667 1 5013 3 chr4A.!!$R1 5012
15 TraesCS4D01G067700 chr1D 55615840 55619489 3649 True 637.500000 706 92.655000 3980 5017 2 chr1D.!!$R1 1037

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
98 102 0.914417 TCCGGCCCATTCTCCTTCTT 60.914 55.000 0.00 0.00 0.00 2.52 F
1754 1813 0.037697 TATTTGCCAGCACGAGTCGT 60.038 50.000 13.56 13.56 42.36 4.34 F
1940 2000 1.134818 ACGGCTGCACTTTCGATATCA 60.135 47.619 0.50 0.00 0.00 2.15 F
1982 2042 1.167851 ATGTGCAATGGACTCAACCG 58.832 50.000 6.43 0.00 0.00 4.44 F
3650 3935 2.362889 GGCCAATGGGTGACAGGG 60.363 66.667 0.00 0.00 36.17 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1788 1847 0.037232 GCAACCAACTCTACCTCGCT 60.037 55.000 0.00 0.0 0.00 4.93 R
3407 3672 3.221771 TGAAGGGATTCCACACACAAAG 58.778 45.455 4.80 0.0 34.83 2.77 R
3593 3859 3.595691 GACCATGCCGTCCTATCAG 57.404 57.895 0.00 0.0 0.00 2.90 R
3832 4372 7.814107 TCTTCAAATTCATCTTGCATACCAAAC 59.186 33.333 0.00 0.0 31.94 2.93 R
4512 5603 2.022129 CGAGTCGTGGGTGTTCTGC 61.022 63.158 3.82 0.0 0.00 4.26 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
96 100 1.147153 CTCCGGCCCATTCTCCTTC 59.853 63.158 0.00 0.00 0.00 3.46
98 102 0.914417 TCCGGCCCATTCTCCTTCTT 60.914 55.000 0.00 0.00 0.00 2.52
220 224 2.816411 TCATCAGAACCCTAACCGTCT 58.184 47.619 0.00 0.00 0.00 4.18
673 677 3.123620 CTGCTCGTCTTGCTGGGC 61.124 66.667 0.00 0.00 0.00 5.36
749 759 3.060615 GGGGTTGCTGCTGCTCTG 61.061 66.667 17.00 0.00 40.48 3.35
999 1035 1.111277 GAGGAGAGAGAGTTCCAGCC 58.889 60.000 0.00 0.00 35.88 4.85
1014 1050 3.521796 GCCATGGAAGAAGCGGCC 61.522 66.667 18.40 0.00 36.73 6.13
1125 1164 4.756458 GAGGACGCTGCTGCTGCT 62.756 66.667 25.43 14.57 40.48 4.24
1212 1251 4.097361 GACCAGTTCCGCTCCCCC 62.097 72.222 0.00 0.00 0.00 5.40
1225 1267 4.421554 CCCCCTGCTCCTCCTCCA 62.422 72.222 0.00 0.00 0.00 3.86
1320 1362 2.223829 CCTCCGCATGTTCTACCTGTAG 60.224 54.545 0.00 0.00 34.56 2.74
1371 1413 1.482593 ACCTTCTTATGCCCTCGACTG 59.517 52.381 0.00 0.00 0.00 3.51
1443 1485 4.385405 GAGCACACCGCAGAGGCT 62.385 66.667 0.00 0.00 46.52 4.58
1477 1524 2.127003 GTGCGCCGCCTGTTTTAC 60.127 61.111 6.63 0.00 0.00 2.01
1495 1551 2.352422 AGCTTGAATGGCTGCCGA 59.648 55.556 14.98 3.61 38.73 5.54
1655 1714 2.494059 CTTCCTTTGTCATGTCACGGT 58.506 47.619 0.00 0.00 0.00 4.83
1659 1718 0.181587 TTTGTCATGTCACGGTGGGT 59.818 50.000 8.50 0.00 0.00 4.51
1660 1719 0.181587 TTGTCATGTCACGGTGGGTT 59.818 50.000 8.50 0.00 0.00 4.11
1661 1720 0.533978 TGTCATGTCACGGTGGGTTG 60.534 55.000 8.50 3.81 0.00 3.77
1662 1721 1.599518 TCATGTCACGGTGGGTTGC 60.600 57.895 8.50 0.00 0.00 4.17
1663 1722 1.896183 CATGTCACGGTGGGTTGCA 60.896 57.895 8.50 1.13 0.00 4.08
1686 1745 2.421073 TGCATTGCAATCTGTACAGCTC 59.579 45.455 18.45 7.19 34.76 4.09
1706 1765 3.220940 TCTGGTGAATGCAAATGTGTCA 58.779 40.909 0.00 0.00 0.00 3.58
1742 1801 0.527565 CAGCCACCTGTGTATTTGCC 59.472 55.000 0.00 0.00 34.31 4.52
1748 1807 0.168788 CCTGTGTATTTGCCAGCACG 59.831 55.000 0.00 0.00 34.86 5.34
1754 1813 0.037697 TATTTGCCAGCACGAGTCGT 60.038 50.000 13.56 13.56 42.36 4.34
1778 1837 2.158310 TCATCCGATACACCTCTGGGAT 60.158 50.000 0.00 0.00 34.73 3.85
1788 1847 2.531428 TCTGGGATGCCACCACCA 60.531 61.111 0.00 0.00 33.63 4.17
1820 1879 2.766970 TGGTTGCTTACGCTTTGTTC 57.233 45.000 0.00 0.00 36.97 3.18
1839 1898 4.696402 TGTTCCGTTTGGTGTATGGATAAC 59.304 41.667 0.00 0.00 36.30 1.89
1846 1905 3.537580 TGGTGTATGGATAACGAAAGGC 58.462 45.455 0.00 0.00 0.00 4.35
1934 1994 1.324736 GAGATAACGGCTGCACTTTCG 59.675 52.381 0.50 0.00 0.00 3.46
1940 2000 1.134818 ACGGCTGCACTTTCGATATCA 60.135 47.619 0.50 0.00 0.00 2.15
1978 2038 3.008923 TCCAAGTATGTGCAATGGACTCA 59.991 43.478 6.43 0.00 35.33 3.41
1982 2042 1.167851 ATGTGCAATGGACTCAACCG 58.832 50.000 6.43 0.00 0.00 4.44
2228 2296 5.881923 ACTGGTAAGTGAAAGTTCCACTA 57.118 39.130 0.00 0.00 43.42 2.74
2229 2297 6.243216 ACTGGTAAGTGAAAGTTCCACTAA 57.757 37.500 0.00 0.00 43.42 2.24
2231 2299 6.710744 ACTGGTAAGTGAAAGTTCCACTAATG 59.289 38.462 0.00 0.00 43.42 1.90
2235 2321 7.227910 GGTAAGTGAAAGTTCCACTAATGTTGA 59.772 37.037 0.00 0.00 43.42 3.18
2238 2324 8.237811 AGTGAAAGTTCCACTAATGTTGATTT 57.762 30.769 0.00 0.00 42.51 2.17
2338 2425 5.048713 GGTTGTCTGTTTAAGGATTCACCAG 60.049 44.000 0.00 0.00 42.04 4.00
2415 2666 9.758651 ACAGGTTAAGTTTACCAATGATTTTTC 57.241 29.630 13.29 0.00 38.16 2.29
2428 2679 7.759433 ACCAATGATTTTTCGTATGATGAAACC 59.241 33.333 0.00 0.00 33.26 3.27
2453 2704 8.879759 CCGTGAGTAACAATGTCAGTTTATTAT 58.120 33.333 0.00 0.00 0.00 1.28
2526 2777 7.967890 ATTTTTGCCTAATCAAACTCCAAAG 57.032 32.000 0.00 0.00 35.86 2.77
2527 2778 6.478512 TTTTGCCTAATCAAACTCCAAAGT 57.521 33.333 0.00 0.00 35.86 2.66
2659 2918 7.549147 TGTGACTAGGACCAGTAGTTTAAAT 57.451 36.000 0.00 0.00 30.60 1.40
2749 3010 6.975772 CGGGTTTTTATCAGTTCAAGTTTTGA 59.024 34.615 0.00 0.00 38.04 2.69
3407 3672 7.135089 GACTTTTGTCTAACTCTTCCCATTC 57.865 40.000 0.00 0.00 45.55 2.67
3593 3859 7.973601 ACCTTTGAAACATGATTTTTGTGTTC 58.026 30.769 0.00 0.00 35.19 3.18
3594 3860 7.823799 ACCTTTGAAACATGATTTTTGTGTTCT 59.176 29.630 0.00 0.00 35.19 3.01
3597 3863 8.945481 TTGAAACATGATTTTTGTGTTCTGAT 57.055 26.923 0.00 0.00 35.19 2.90
3650 3935 2.362889 GGCCAATGGGTGACAGGG 60.363 66.667 0.00 0.00 36.17 4.45
4124 5000 0.179018 GTGGGTGAGCAAGAACTGGT 60.179 55.000 0.00 0.00 38.89 4.00
4192 5068 0.393808 GCCGGCTTATCCTGTTCCAA 60.394 55.000 22.15 0.00 0.00 3.53
4243 5123 3.774766 AGCTGGTGAACCATGATAGTACA 59.225 43.478 1.88 0.00 46.46 2.90
4512 5603 5.398122 CCGCAATACTTGTACTTTGTGTTTG 59.602 40.000 0.00 1.80 0.00 2.93
4538 5630 0.892755 ACCCACGACTCGAGCATAAA 59.107 50.000 13.61 0.00 0.00 1.40
4609 8454 9.606631 AACTTGTAGAACAAAAATGGCATTAAA 57.393 25.926 14.05 0.00 37.69 1.52
4638 8484 3.751479 AAAATGGCACCCTTCAAAGAC 57.249 42.857 0.00 0.00 0.00 3.01
4686 8683 7.068593 TGCAATTCTAGGGACCAATATTTTCAG 59.931 37.037 0.00 0.00 0.00 3.02
4697 8694 9.136323 GGACCAATATTTTCAGAATTATCAGGT 57.864 33.333 0.00 0.00 30.44 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
85 86 2.443958 GGGGGAAAGAAGGAGAATGG 57.556 55.000 0.00 0.00 0.00 3.16
189 193 1.003116 GTTCTGATGATGTGATGCGGC 60.003 52.381 0.00 0.00 0.00 6.53
749 759 3.992317 GGTAGATCCGGCGAGGCC 61.992 72.222 9.30 0.00 46.75 5.19
958 970 2.653702 GCAGAGCGACCAGACTGT 59.346 61.111 0.93 0.00 33.57 3.55
999 1035 2.125147 TCGGCCGCTTCTTCCATG 60.125 61.111 23.51 0.00 0.00 3.66
1048 1084 2.578163 TTCTCCGCCGCATCCTCAAG 62.578 60.000 0.00 0.00 0.00 3.02
1050 1086 3.074369 TTCTCCGCCGCATCCTCA 61.074 61.111 0.00 0.00 0.00 3.86
1212 1251 2.856039 TACCGGTGGAGGAGGAGCAG 62.856 65.000 19.93 0.00 34.73 4.24
1225 1267 0.981943 CCCTTGAGGAAGTTACCGGT 59.018 55.000 13.98 13.98 38.24 5.28
1371 1413 2.070028 GAGAAAGGAACAAGGAGCGTC 58.930 52.381 0.00 0.00 0.00 5.19
1655 1714 4.697592 GCAATGCAATGCAACCCA 57.302 50.000 21.74 0.00 43.62 4.51
1675 1734 2.354103 GCATTCACCAGAGCTGTACAGA 60.354 50.000 27.08 2.12 0.00 3.41
1686 1745 3.646611 TGACACATTTGCATTCACCAG 57.353 42.857 0.00 0.00 0.00 4.00
1706 1765 2.028748 GGCTGGATCTGCAAAACAACAT 60.029 45.455 11.94 0.00 0.00 2.71
1748 1807 3.556513 GTGTATCGGATGATCACGACTC 58.443 50.000 10.25 7.51 42.39 3.36
1754 1813 2.893489 CCAGAGGTGTATCGGATGATCA 59.107 50.000 0.00 0.00 35.99 2.92
1788 1847 0.037232 GCAACCAACTCTACCTCGCT 60.037 55.000 0.00 0.00 0.00 4.93
1820 1879 3.523547 TCGTTATCCATACACCAAACGG 58.476 45.455 5.69 0.00 39.92 4.44
1839 1898 2.042686 TCATCAGAATGGGCCTTTCG 57.957 50.000 22.16 17.57 36.16 3.46
1846 1905 4.647853 ACCACAATGAATCATCAGAATGGG 59.352 41.667 0.00 0.00 39.39 4.00
1978 2038 2.030893 CACAAATGCAGATCACACGGTT 60.031 45.455 0.00 0.00 0.00 4.44
1982 2042 5.107109 TGTAACACAAATGCAGATCACAC 57.893 39.130 0.00 0.00 0.00 3.82
2081 2148 3.224269 CATCCACCATATCCATGTTGCA 58.776 45.455 0.00 0.00 0.00 4.08
2082 2149 3.225104 ACATCCACCATATCCATGTTGC 58.775 45.455 0.00 0.00 0.00 4.17
2228 2296 8.297470 ACCATATGCTGTCTTAAATCAACATT 57.703 30.769 0.00 0.00 0.00 2.71
2229 2297 7.886629 ACCATATGCTGTCTTAAATCAACAT 57.113 32.000 0.00 0.00 0.00 2.71
2231 2299 8.243426 TGAAACCATATGCTGTCTTAAATCAAC 58.757 33.333 0.00 0.00 0.00 3.18
2235 2321 7.944729 ACTGAAACCATATGCTGTCTTAAAT 57.055 32.000 0.00 0.00 0.00 1.40
2238 2324 5.647658 CCAACTGAAACCATATGCTGTCTTA 59.352 40.000 0.00 0.00 0.00 2.10
2382 2469 7.883391 TTGGTAAACTTAACCTGTCATGAAA 57.117 32.000 0.00 0.00 37.91 2.69
2391 2641 8.635328 ACGAAAAATCATTGGTAAACTTAACCT 58.365 29.630 0.00 0.00 37.91 3.50
2392 2642 8.806177 ACGAAAAATCATTGGTAAACTTAACC 57.194 30.769 0.00 0.00 37.53 2.85
2415 2666 4.860352 TGTTACTCACGGTTTCATCATACG 59.140 41.667 0.00 0.00 0.00 3.06
2428 2679 9.901724 GATAATAAACTGACATTGTTACTCACG 57.098 33.333 0.00 0.00 0.00 4.35
2453 2704 9.452287 TCAAGATTTCATTCATCAGTATTGTGA 57.548 29.630 0.00 0.00 0.00 3.58
2525 2776 4.386711 GTCCTGGCACAAAGTTACTTACT 58.613 43.478 0.00 0.00 38.70 2.24
2526 2777 3.501062 GGTCCTGGCACAAAGTTACTTAC 59.499 47.826 0.00 0.00 38.70 2.34
2527 2778 3.393278 AGGTCCTGGCACAAAGTTACTTA 59.607 43.478 0.00 0.00 38.70 2.24
2588 2847 5.177142 GTGAAAGTCCTTCCGAAGTTCTAAC 59.823 44.000 7.37 4.28 32.53 2.34
3393 3656 5.530915 CACACACAAAGAATGGGAAGAGTTA 59.469 40.000 0.00 0.00 35.35 2.24
3407 3672 3.221771 TGAAGGGATTCCACACACAAAG 58.778 45.455 4.80 0.00 34.83 2.77
3593 3859 3.595691 GACCATGCCGTCCTATCAG 57.404 57.895 0.00 0.00 0.00 2.90
3832 4372 7.814107 TCTTCAAATTCATCTTGCATACCAAAC 59.186 33.333 0.00 0.00 31.94 2.93
4192 5068 2.489275 CCCGGCAAAGTTGTGTGCT 61.489 57.895 0.00 0.00 40.70 4.40
4400 5289 2.297701 TGGGAAGTCAGAGCAAACAAC 58.702 47.619 0.00 0.00 0.00 3.32
4512 5603 2.022129 CGAGTCGTGGGTGTTCTGC 61.022 63.158 3.82 0.00 0.00 4.26
4538 5630 8.284945 AGAACATGATAGTTAATGTGTTGCAT 57.715 30.769 0.00 0.00 37.11 3.96
4609 8454 4.639078 AGGGTGCCATTTTAGCAAAATT 57.361 36.364 4.70 0.00 43.02 1.82
4638 8484 2.932614 CTCGACTAAGCCTGAAATGTGG 59.067 50.000 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.