Multiple sequence alignment - TraesCS7D01G198800

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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 TraesCS7D01G198800 chr7D 100.000 2474 0 0 1 2474 155686979 155689452 0.000000e+00 4569.0
1 TraesCS7D01G198800 chr2A 96.016 2485 76 9 1 2474 575062871 575060399 0.000000e+00 4019.0
2 TraesCS7D01G198800 chrUn 87.449 972 66 21 1506 2474 504592 503674 0.000000e+00 1068.0
3 TraesCS7D01G198800 chr1B 77.596 183 33 5 1136 1314 168981774 168981952 1.210000e-18 104.0
4 TraesCS7D01G198800 chr7A 82.727 110 17 2 1202 1311 687819381 687819488 2.030000e-16 97.1
5 TraesCS7D01G198800 chr7A 82.857 105 17 1 1198 1302 102905147 102905250 2.620000e-15 93.5
6 TraesCS7D01G198800 chr5A 83.673 98 14 2 1214 1311 34104311 34104216 9.420000e-15 91.6
7 TraesCS7D01G198800 chr6B 77.778 117 20 6 1197 1311 63104909 63104797 1.590000e-07 67.6


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 TraesCS7D01G198800 chr7D 155686979 155689452 2473 False 4569 4569 100.000 1 2474 1 chr7D.!!$F1 2473
1 TraesCS7D01G198800 chr2A 575060399 575062871 2472 True 4019 4019 96.016 1 2474 1 chr2A.!!$R1 2473
2 TraesCS7D01G198800 chrUn 503674 504592 918 True 1068 1068 87.449 1506 2474 1 chrUn.!!$R1 968

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
352 355 1.749063 ACATCGTAGATGGTTCGCTGA 59.251 47.619 13.69 0.0 45.12 4.26 F
529 532 1.882912 ATTGCGCGTGATATGATGGT 58.117 45.000 8.43 0.0 0.00 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1153 1157 0.249911 ACAACACGAGAGCTGTTCCC 60.250 55.0 0.0 0.0 34.65 3.97 R
2099 2117 0.835543 AGCAGAGGAAGGTCAGTGCT 60.836 55.0 0.0 0.0 36.44 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
34 35 7.112122 TCAATATCTCTTGCCTTGAAGCTTTA 58.888 34.615 0.00 0.00 0.00 1.85
38 39 6.299805 TCTCTTGCCTTGAAGCTTTATCTA 57.700 37.500 0.00 0.00 0.00 1.98
97 98 1.922135 ATTGCTACGCGTTTGGGCTG 61.922 55.000 20.78 0.40 0.00 4.85
104 105 2.358247 CGTTTGGGCTGGCGTAGT 60.358 61.111 0.00 0.00 0.00 2.73
121 122 3.553096 CGTAGTCTCATGGCCCTCATTAC 60.553 52.174 0.00 0.00 32.92 1.89
157 158 2.274437 CTAGAAGCAGCTTCAATCGCA 58.726 47.619 32.20 12.06 42.37 5.10
227 230 3.308438 AAATTCAGAGCACAACCATGC 57.692 42.857 0.00 0.00 46.50 4.06
351 354 2.209838 ACATCGTAGATGGTTCGCTG 57.790 50.000 13.69 0.00 45.12 5.18
352 355 1.749063 ACATCGTAGATGGTTCGCTGA 59.251 47.619 13.69 0.00 45.12 4.26
390 393 6.183360 CCAATGTTTTCTTTGGTCTGTTGTTG 60.183 38.462 0.00 0.00 44.80 3.33
429 432 7.365497 AGGGAATCATCTTTTGTGTTCTTTT 57.635 32.000 0.00 0.00 0.00 2.27
434 437 5.350633 TCATCTTTTGTGTTCTTTTGCAGG 58.649 37.500 0.00 0.00 0.00 4.85
508 511 9.943163 TTTTCTTGGCAATTTAATGTTTAAAGC 57.057 25.926 0.00 0.00 0.00 3.51
516 519 7.459991 GCAATTTAATGTTTAAAGCAATTGCGC 60.460 33.333 24.02 11.38 42.81 6.09
526 529 2.320805 GCAATTGCGCGTGATATGAT 57.679 45.000 15.87 0.00 0.00 2.45
529 532 1.882912 ATTGCGCGTGATATGATGGT 58.117 45.000 8.43 0.00 0.00 3.55
552 555 8.944138 TGGTCAGATTAATTAAGATGTGGGATA 58.056 33.333 3.94 0.00 0.00 2.59
598 601 7.442666 ACTTACTTGATGAAGAGGTCAGTTTTC 59.557 37.037 0.00 0.00 40.43 2.29
670 673 7.037586 ACAAAAATACTAGGACATCTTCTCCCA 60.038 37.037 0.00 0.00 0.00 4.37
768 771 7.215085 TCCAAGAAGGTTCAGTCTAAGTTTAC 58.785 38.462 0.00 0.00 39.02 2.01
982 986 8.293157 TCATTAAAGCATACAAATGTCGAACAA 58.707 29.630 0.00 0.00 35.38 2.83
1216 1220 6.768381 GGAAAATGAGGGTAGTATGGAGAAAG 59.232 42.308 0.00 0.00 0.00 2.62
1278 1282 7.551585 AGTATATAATAGCTCACAGATGTGGC 58.448 38.462 12.77 13.87 45.65 5.01
1365 1369 6.457355 TGCATGTTCTTTCATAGTTTTGCAT 58.543 32.000 0.00 0.00 0.00 3.96
1375 1384 9.630098 CTTTCATAGTTTTGCATGTCTAATTGT 57.370 29.630 0.00 0.00 0.00 2.71
1424 1433 8.655970 AGTGCAAAACTTATTTGTTCTGAAAAC 58.344 29.630 0.00 0.00 34.57 2.43
1467 1476 2.771943 TGATGAACTCCACCTCCATACC 59.228 50.000 0.00 0.00 0.00 2.73
1563 1572 7.106890 TCAGGTGTTGATATAAAATCACCGAA 58.893 34.615 6.86 0.00 46.50 4.30
1564 1573 7.608376 TCAGGTGTTGATATAAAATCACCGAAA 59.392 33.333 6.86 0.00 46.50 3.46
1565 1574 8.405531 CAGGTGTTGATATAAAATCACCGAAAT 58.594 33.333 6.86 0.00 46.50 2.17
1566 1575 9.621629 AGGTGTTGATATAAAATCACCGAAATA 57.378 29.630 6.86 0.00 46.50 1.40
1640 1655 7.093068 TGGAACAGGTACAAGCATTCTTATCTA 60.093 37.037 0.00 0.00 0.00 1.98
1699 1714 3.615224 AAATTGTTCCACCATCCATGC 57.385 42.857 0.00 0.00 0.00 4.06
1713 1728 0.798776 CCATGCGTCACAGTTTCTCC 59.201 55.000 0.00 0.00 0.00 3.71
1879 1894 4.038642 GCAAGGGGTAACAACTGATTTCAA 59.961 41.667 0.00 0.00 39.74 2.69
2022 2037 4.529377 ACCCTGAAATTCACATGCAGATTT 59.471 37.500 0.00 0.00 0.00 2.17
2084 2102 8.353684 CCACAGTACAACAATAACCATTTTACA 58.646 33.333 0.00 0.00 0.00 2.41
2099 2117 7.116075 ACCATTTTACATGTTGTATCTGCCTA 58.884 34.615 2.30 0.00 32.20 3.93
2262 2281 2.485677 CAGGACATCTGCGCCAAAT 58.514 52.632 4.18 0.00 36.60 2.32
2264 2283 0.035152 AGGACATCTGCGCCAAATGA 60.035 50.000 17.39 4.16 0.00 2.57
2325 2344 8.725405 TGTTACTGATCTAAAAAGACACACAA 57.275 30.769 0.00 0.00 0.00 3.33
2442 2461 5.296035 GGGACTAATTTGAGTTAACCATCGG 59.704 44.000 0.88 0.00 0.00 4.18
2471 2490 6.295249 TGTGCAATGAAGATCGGGATAATTA 58.705 36.000 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 3.508012 GTCATCCGGTAGCTCACATAGAT 59.492 47.826 0.00 0.00 0.00 1.98
38 39 0.753262 GGTCATCCGGTAGCTCACAT 59.247 55.000 0.00 0.00 0.00 3.21
97 98 2.109181 GGGCCATGAGACTACGCC 59.891 66.667 4.39 0.00 38.96 5.68
104 105 1.770658 CCTGTAATGAGGGCCATGAGA 59.229 52.381 6.18 0.00 35.24 3.27
157 158 1.688772 GTGCATGCATCCCATTCTCT 58.311 50.000 25.64 0.00 29.71 3.10
227 230 1.278985 TGTGTAAGCTCACCTGATGGG 59.721 52.381 3.31 0.00 37.51 4.00
228 231 2.768253 TGTGTAAGCTCACCTGATGG 57.232 50.000 3.31 0.00 37.51 3.51
351 354 6.599638 AGAAAACATTGGCACCTAGTTAGATC 59.400 38.462 0.00 0.00 0.00 2.75
352 355 6.485171 AGAAAACATTGGCACCTAGTTAGAT 58.515 36.000 0.00 0.00 0.00 1.98
383 386 2.090760 ACATGCACAGTGACAACAACA 58.909 42.857 4.15 0.00 0.00 3.33
390 393 2.472695 TCCCTAACATGCACAGTGAC 57.527 50.000 4.15 0.00 0.00 3.67
508 511 2.031769 ACCATCATATCACGCGCAATTG 60.032 45.455 5.73 0.00 0.00 2.32
526 529 7.206789 TCCCACATCTTAATTAATCTGACCA 57.793 36.000 11.90 0.00 0.00 4.02
529 532 8.944138 TGGTATCCCACATCTTAATTAATCTGA 58.056 33.333 11.90 2.22 35.17 3.27
552 555 6.930667 AAGTTCACTGTTAACGTTAATGGT 57.069 33.333 22.65 19.48 32.00 3.55
598 601 9.800433 TGTATAATGTTTATGTTGGCAAATCAG 57.200 29.630 0.00 0.00 0.00 2.90
603 606 9.800433 CTGATTGTATAATGTTTATGTTGGCAA 57.200 29.630 0.00 0.00 0.00 4.52
649 652 7.510675 TTTTGGGAGAAGATGTCCTAGTATT 57.489 36.000 0.00 0.00 34.16 1.89
651 654 7.510675 AATTTTGGGAGAAGATGTCCTAGTA 57.489 36.000 0.00 0.00 34.16 1.82
652 655 6.394345 AATTTTGGGAGAAGATGTCCTAGT 57.606 37.500 0.00 0.00 34.16 2.57
653 656 8.986929 AATAATTTTGGGAGAAGATGTCCTAG 57.013 34.615 0.00 0.00 34.16 3.02
655 658 9.942526 AATAATAATTTTGGGAGAAGATGTCCT 57.057 29.630 0.00 0.00 34.16 3.85
656 659 9.971922 CAATAATAATTTTGGGAGAAGATGTCC 57.028 33.333 0.00 0.00 0.00 4.02
697 700 8.494433 ACCATATGTTACATTACCTTCTCATGT 58.506 33.333 2.23 0.00 35.33 3.21
721 724 2.094182 TCAGCGACTGGACTTGATAACC 60.094 50.000 6.95 0.00 31.51 2.85
732 735 1.649664 CTTCTTGGATCAGCGACTGG 58.350 55.000 6.95 0.00 31.51 4.00
768 771 3.130633 TGATGGAAATACGGCGAAGATG 58.869 45.455 16.62 0.00 0.00 2.90
935 939 4.024893 TGACGTGTCTTCTTCAAAATCTGC 60.025 41.667 0.00 0.00 0.00 4.26
982 986 5.256474 CCTCATGGTGGAAATAACAGAACT 58.744 41.667 0.00 0.00 0.00 3.01
996 1000 6.319658 ACAAAACAATATAGAGCCTCATGGTG 59.680 38.462 0.00 0.00 35.27 4.17
1095 1099 0.403271 AGTCTGCCTGCTGTCCATTT 59.597 50.000 0.00 0.00 0.00 2.32
1153 1157 0.249911 ACAACACGAGAGCTGTTCCC 60.250 55.000 0.00 0.00 34.65 3.97
1163 1167 2.603110 CCATCGGAATGTACAACACGAG 59.397 50.000 19.07 13.01 29.83 4.18
1191 1195 5.888982 TCTCCATACTACCCTCATTTTCC 57.111 43.478 0.00 0.00 0.00 3.13
1278 1282 3.364889 TCTGGTATTCTACGAATGCCG 57.635 47.619 15.62 11.63 45.44 5.69
1375 1384 4.978099 TGCCCCTGCAAAATCATTTTTAA 58.022 34.783 0.00 0.00 46.66 1.52
1419 1428 4.634443 TCCGGCTCTTGCTTTATAGTTTTC 59.366 41.667 0.00 0.00 39.59 2.29
1424 1433 2.365617 TCCTCCGGCTCTTGCTTTATAG 59.634 50.000 0.00 0.00 39.59 1.31
1467 1476 4.477213 TCCTTCCCCTAATCCTTTTAGGTG 59.523 45.833 9.83 0.13 39.86 4.00
1563 1572 9.988815 GACACACTGGACATTCTATATCTTATT 57.011 33.333 0.00 0.00 0.00 1.40
1564 1573 8.589338 GGACACACTGGACATTCTATATCTTAT 58.411 37.037 0.00 0.00 0.00 1.73
1565 1574 7.785028 AGGACACACTGGACATTCTATATCTTA 59.215 37.037 0.00 0.00 0.00 2.10
1566 1575 6.613271 AGGACACACTGGACATTCTATATCTT 59.387 38.462 0.00 0.00 0.00 2.40
1567 1576 6.041409 CAGGACACACTGGACATTCTATATCT 59.959 42.308 0.00 0.00 34.84 1.98
1568 1577 6.219473 CAGGACACACTGGACATTCTATATC 58.781 44.000 0.00 0.00 34.84 1.63
1615 1630 6.116126 AGATAAGAATGCTTGTACCTGTTCC 58.884 40.000 0.00 0.00 35.56 3.62
1678 1693 3.130164 CGCATGGATGGTGGAACAATTTA 59.870 43.478 0.00 0.00 44.16 1.40
1699 1714 1.889829 AGAGAGGGAGAAACTGTGACG 59.110 52.381 0.00 0.00 0.00 4.35
1713 1728 0.835941 ATGCAAGCAGGGTAGAGAGG 59.164 55.000 0.00 0.00 0.00 3.69
1879 1894 7.660112 TGCAAACATAACTCATCTTGATTGTT 58.340 30.769 0.00 0.00 0.00 2.83
1900 1915 5.414144 TCTCAAATTCATAACCGTGATGCAA 59.586 36.000 0.00 0.00 0.00 4.08
1996 2011 1.133025 GCATGTGAATTTCAGGGTCCG 59.867 52.381 0.00 0.00 0.00 4.79
2084 2102 3.452264 TCAGTGCTAGGCAGATACAACAT 59.548 43.478 0.00 0.00 40.08 2.71
2099 2117 0.835543 AGCAGAGGAAGGTCAGTGCT 60.836 55.000 0.00 0.00 36.44 4.40
2239 2258 0.955428 GGCGCAGATGTCCTGTCAAA 60.955 55.000 10.83 0.00 44.71 2.69
2262 2281 1.162181 CGGCGGTCTCGGTAGTATCA 61.162 60.000 0.00 0.00 36.79 2.15
2264 2283 1.146930 TCGGCGGTCTCGGTAGTAT 59.853 57.895 7.21 0.00 36.79 2.12
2325 2344 5.778750 AGACACACCACAGGTACTACTAATT 59.221 40.000 0.00 0.00 36.02 1.40
2328 2347 4.330250 GAGACACACCACAGGTACTACTA 58.670 47.826 0.00 0.00 36.02 1.82
2442 2461 4.107622 CCCGATCTTCATTGCACATTTTC 58.892 43.478 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.