Multiple sequence alignment - TraesCS4A01G441400

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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 TraesCS4A01G441400 chr4A 100.000 3466 0 0 1 3466 709893624 709897089 0 6401
1 TraesCS4A01G441400 chr7D 93.377 3397 166 33 1 3373 25399174 25402535 0 4972
2 TraesCS4A01G441400 chr7A 92.106 3509 175 38 1 3464 26415650 26419101 0 4852


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 TraesCS4A01G441400 chr4A 709893624 709897089 3465 False 6401 6401 100.000 1 3466 1 chr4A.!!$F1 3465
1 TraesCS4A01G441400 chr7D 25399174 25402535 3361 False 4972 4972 93.377 1 3373 1 chr7D.!!$F1 3372
2 TraesCS4A01G441400 chr7A 26415650 26419101 3451 False 4852 4852 92.106 1 3464 1 chr7A.!!$F1 3463

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
53 54 1.374758 CTCGCCACCTGTGAAGGAC 60.375 63.158 0.0 0.0 31.89 3.85 F
1589 1616 0.103937 GGCGATGAAGAGGAGGTGAG 59.896 60.000 0.0 0.0 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1684 1711 0.110678 CATCATCATCCTGCCCAGCT 59.889 55.0 0.0 0.0 0.0 4.24 R
3037 3082 0.034059 AGAGTGTGAGTTGGCTTCGG 59.966 55.0 0.0 0.0 0.0 4.30 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
37 38 2.669364 CATGCAGTGAACCTTTTGCTC 58.331 47.619 0.00 0.00 37.45 4.26
53 54 1.374758 CTCGCCACCTGTGAAGGAC 60.375 63.158 0.00 0.00 31.89 3.85
172 175 9.725019 CAGGAATTCCTAGTGCATATGTTTATA 57.275 33.333 26.61 0.00 46.65 0.98
254 259 9.129532 AGGAAGAAAATAAAGGCAGATCATAAG 57.870 33.333 0.00 0.00 0.00 1.73
332 337 6.553100 CAGAGACAGGAGGATTATCTTTAGGT 59.447 42.308 0.00 0.00 0.00 3.08
334 339 6.444704 AGACAGGAGGATTATCTTTAGGTCA 58.555 40.000 0.00 0.00 0.00 4.02
335 340 6.553100 AGACAGGAGGATTATCTTTAGGTCAG 59.447 42.308 0.00 0.00 0.00 3.51
667 686 5.064071 GGAGAAAAAGTAAGCATCTCTTCCG 59.936 44.000 0.00 0.00 37.33 4.30
806 826 4.394300 CCTCCTCAGAAATTGTTACTGCTG 59.606 45.833 0.00 0.00 0.00 4.41
809 829 4.937620 CCTCAGAAATTGTTACTGCTGCTA 59.062 41.667 0.00 0.00 0.00 3.49
828 848 6.072112 TGCTACTTTTGCTTGTTCTAAAGG 57.928 37.500 0.00 0.00 34.60 3.11
829 849 5.009610 TGCTACTTTTGCTTGTTCTAAAGGG 59.990 40.000 0.00 0.00 34.60 3.95
844 864 7.674348 TGTTCTAAAGGGAGAGACAGAGAATTA 59.326 37.037 0.00 0.00 0.00 1.40
917 937 5.335976 GGTTGGAATGAACCTGCTTCTTAAG 60.336 44.000 0.00 0.00 42.03 1.85
990 1010 4.030452 GTGGTTGCTGCCTGACGC 62.030 66.667 0.00 0.00 38.31 5.19
1062 1085 4.373116 CACTACAGCACCGCCGGT 62.373 66.667 1.02 1.02 35.62 5.28
1126 1149 5.003804 GTGATGTTCTTCAACACCAGGTAT 58.996 41.667 0.00 0.00 45.47 2.73
1128 1151 4.431416 TGTTCTTCAACACCAGGTATGT 57.569 40.909 0.00 0.00 37.61 2.29
1138 1161 9.521841 TTCAACACCAGGTATGTTTCATATTAA 57.478 29.630 0.00 0.00 38.22 1.40
1141 1164 9.474313 AACACCAGGTATGTTTCATATTAACAT 57.526 29.630 14.27 14.27 45.45 2.71
1142 1165 9.120538 ACACCAGGTATGTTTCATATTAACATC 57.879 33.333 13.55 7.98 43.24 3.06
1217 1240 9.567848 TCAAAAGTAACAGTTCTGATTTGTTTC 57.432 29.630 6.83 7.56 36.52 2.78
1329 1352 1.163554 GCAGCAGAAACCTCAGGAAG 58.836 55.000 0.00 0.00 0.00 3.46
1336 1359 4.314121 CAGAAACCTCAGGAAGTTCAGAG 58.686 47.826 0.00 14.43 0.00 3.35
1417 1440 2.029964 GACACGCCTCCCAACGAA 59.970 61.111 0.00 0.00 0.00 3.85
1458 1481 6.144854 CGCAATTCTTTTGATTCAGTTCAGA 58.855 36.000 0.00 0.00 0.00 3.27
1459 1482 6.304922 CGCAATTCTTTTGATTCAGTTCAGAG 59.695 38.462 0.00 0.00 0.00 3.35
1464 1487 6.595682 TCTTTTGATTCAGTTCAGAGAAGGT 58.404 36.000 0.00 0.00 0.00 3.50
1499 1526 9.668497 CTGATCATCATCTGATATATTGGTGTT 57.332 33.333 0.00 0.00 44.83 3.32
1500 1527 9.662947 TGATCATCATCTGATATATTGGTGTTC 57.337 33.333 0.00 0.00 44.83 3.18
1507 1534 6.946340 TCTGATATATTGGTGTTCTGTGTGT 58.054 36.000 0.00 0.00 0.00 3.72
1508 1535 6.818142 TCTGATATATTGGTGTTCTGTGTGTG 59.182 38.462 0.00 0.00 0.00 3.82
1511 1538 8.097662 TGATATATTGGTGTTCTGTGTGTGTTA 58.902 33.333 0.00 0.00 0.00 2.41
1521 1548 7.218204 GTGTTCTGTGTGTGTTAAAATTCAGAC 59.782 37.037 0.00 0.00 31.82 3.51
1551 1578 2.186903 CCTTCCCCATCCGACACG 59.813 66.667 0.00 0.00 0.00 4.49
1589 1616 0.103937 GGCGATGAAGAGGAGGTGAG 59.896 60.000 0.00 0.00 0.00 3.51
1590 1617 0.529555 GCGATGAAGAGGAGGTGAGC 60.530 60.000 0.00 0.00 0.00 4.26
1599 1626 6.373759 TGAAGAGGAGGTGAGCTATTATACA 58.626 40.000 0.00 0.00 0.00 2.29
1603 1630 6.841755 AGAGGAGGTGAGCTATTATACAAACT 59.158 38.462 0.00 0.00 0.00 2.66
1628 1655 4.603231 ATTTGCAGTTGCTTGTTTGTTG 57.397 36.364 5.62 0.00 42.66 3.33
1684 1711 4.373116 GAGACCGGTTCGCAGGCA 62.373 66.667 9.42 0.00 35.79 4.75
1972 2005 5.431765 GGAAATGAGAGCAGAGGTTTATCA 58.568 41.667 0.00 0.00 0.00 2.15
2037 2070 3.118445 GGATCAGGGTTCTTCTCAAGGAG 60.118 52.174 0.00 0.00 0.00 3.69
2311 2345 2.156917 CAGCTGGCTCAAGATCAACAA 58.843 47.619 5.57 0.00 0.00 2.83
2378 2412 5.335976 GGTTAGAGAAAAGTCATGGCTTTGG 60.336 44.000 25.17 0.00 38.54 3.28
2404 2438 3.751479 AGTACAGTTGCTGACATGTGA 57.249 42.857 1.15 0.00 35.18 3.58
2406 2440 4.645535 AGTACAGTTGCTGACATGTGATT 58.354 39.130 1.15 0.00 35.18 2.57
2414 2449 5.361135 TGCTGACATGTGATTAACTGTTG 57.639 39.130 1.15 0.00 0.00 3.33
2919 2962 5.634896 GGCAACTCAAGTCAAACATGATAG 58.365 41.667 0.00 0.00 0.00 2.08
3017 3062 8.677300 AGCATGTCATTGTAGGTTAAGTTAATG 58.323 33.333 0.00 0.00 0.00 1.90
3037 3082 2.289444 TGCTACAGGGTTGAACTGCTAC 60.289 50.000 0.00 0.00 39.55 3.58
3039 3084 0.034896 ACAGGGTTGAACTGCTACCG 59.965 55.000 0.00 0.00 42.46 4.02
3059 3104 2.682836 GAAGCCAACTCACACTCTCTC 58.317 52.381 0.00 0.00 0.00 3.20
3069 3114 1.202582 CACACTCTCTCAGGTAACCGG 59.797 57.143 0.00 0.00 37.17 5.28
3115 3160 3.250762 CAGAATGTTCCAGACAGCGAAAA 59.749 43.478 0.00 0.00 42.62 2.29
3235 3280 2.092158 TGGTTTGTCACATGTTCCAGGA 60.092 45.455 0.00 0.00 0.00 3.86
3334 3379 2.960384 TGGAGTCAAACTTAGGTCGACA 59.040 45.455 18.91 0.00 0.00 4.35
3390 3449 1.845627 TTCTTCAGGCCCTCTGCAGG 61.846 60.000 15.13 4.45 43.06 4.85
3411 3470 6.648725 GCAGGTGAACAGGCAAAATATTAAAA 59.351 34.615 0.00 0.00 0.00 1.52
3412 3471 7.334171 GCAGGTGAACAGGCAAAATATTAAAAT 59.666 33.333 0.00 0.00 0.00 1.82
3445 3507 5.329399 TGACTTGGCATATTAACCAAAGGT 58.671 37.500 0.00 0.00 45.03 3.50
3460 3522 6.575162 ACCAAAGGTTAATCACAGATCAAC 57.425 37.500 0.00 0.00 27.29 3.18
3461 3523 6.306987 ACCAAAGGTTAATCACAGATCAACT 58.693 36.000 0.00 0.00 27.29 3.16
3462 3524 6.207417 ACCAAAGGTTAATCACAGATCAACTG 59.793 38.462 0.00 0.00 42.17 3.16
3463 3525 8.658992 ACCAAAGGTTAATCACAGATCAACTGG 61.659 40.741 0.00 0.00 41.29 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 2.669364 GAGCAAAAGGTTCACTGCATG 58.331 47.619 0.00 0.00 37.26 4.06
37 38 2.425592 TGTCCTTCACAGGTGGCG 59.574 61.111 0.00 0.00 41.69 5.69
53 54 2.038295 GCCTGAAGATATCCTGTCCCTG 59.962 54.545 0.00 0.00 0.00 4.45
180 183 5.105064 ACCTGTAGATATGTAAACCGCAACT 60.105 40.000 0.00 0.00 0.00 3.16
181 184 5.114081 ACCTGTAGATATGTAAACCGCAAC 58.886 41.667 0.00 0.00 0.00 4.17
182 185 5.347620 ACCTGTAGATATGTAAACCGCAA 57.652 39.130 0.00 0.00 0.00 4.85
210 213 8.956446 TTCTTCCTCCTTCATTCCTTTTAATT 57.044 30.769 0.00 0.00 0.00 1.40
212 215 8.776061 TTTTCTTCCTCCTTCATTCCTTTTAA 57.224 30.769 0.00 0.00 0.00 1.52
213 216 8.956446 ATTTTCTTCCTCCTTCATTCCTTTTA 57.044 30.769 0.00 0.00 0.00 1.52
214 217 7.862274 ATTTTCTTCCTCCTTCATTCCTTTT 57.138 32.000 0.00 0.00 0.00 2.27
215 218 8.956446 TTATTTTCTTCCTCCTTCATTCCTTT 57.044 30.769 0.00 0.00 0.00 3.11
216 219 8.956446 TTTATTTTCTTCCTCCTTCATTCCTT 57.044 30.769 0.00 0.00 0.00 3.36
217 220 7.617329 CCTTTATTTTCTTCCTCCTTCATTCCT 59.383 37.037 0.00 0.00 0.00 3.36
218 221 7.631594 GCCTTTATTTTCTTCCTCCTTCATTCC 60.632 40.741 0.00 0.00 0.00 3.01
219 222 7.093771 TGCCTTTATTTTCTTCCTCCTTCATTC 60.094 37.037 0.00 0.00 0.00 2.67
222 225 5.640147 TGCCTTTATTTTCTTCCTCCTTCA 58.360 37.500 0.00 0.00 0.00 3.02
269 274 6.207417 CCCAACTGAAACTAACTGTTGATGAT 59.793 38.462 15.36 0.00 44.16 2.45
332 337 3.333980 TGTAGAGGGAGAAAGAGACCTGA 59.666 47.826 0.00 0.00 32.42 3.86
334 339 3.076182 TGTGTAGAGGGAGAAAGAGACCT 59.924 47.826 0.00 0.00 35.67 3.85
335 340 3.432378 TGTGTAGAGGGAGAAAGAGACC 58.568 50.000 0.00 0.00 0.00 3.85
470 488 7.646314 AGTGCTTACTTATATATATACGCGGG 58.354 38.462 12.47 0.00 0.00 6.13
479 497 8.506196 TCCCTCCAAAGTGCTTACTTATATAT 57.494 34.615 0.00 0.00 0.00 0.86
480 498 7.472945 GCTCCCTCCAAAGTGCTTACTTATATA 60.473 40.741 0.00 0.00 0.00 0.86
667 686 6.297582 AGAATCATGAACAGGAGGATTGATC 58.702 40.000 0.00 0.00 0.00 2.92
706 725 2.346847 CGTTGCGATGAAGAGGAGAAAG 59.653 50.000 0.00 0.00 0.00 2.62
782 801 3.691609 GCAGTAACAATTTCTGAGGAGGG 59.308 47.826 0.00 0.00 0.00 4.30
797 817 4.222114 CAAGCAAAAGTAGCAGCAGTAAC 58.778 43.478 0.00 0.00 0.00 2.50
806 826 5.240844 TCCCTTTAGAACAAGCAAAAGTAGC 59.759 40.000 0.00 0.00 0.00 3.58
809 829 5.445964 TCTCCCTTTAGAACAAGCAAAAGT 58.554 37.500 0.00 0.00 0.00 2.66
862 882 3.015327 GAGCATGACAATTCTGCTTCCT 58.985 45.455 0.00 0.00 45.79 3.36
917 937 5.649831 AGTTGGGATCAAAGATAGTTTCTGC 59.350 40.000 0.00 0.00 33.93 4.26
1062 1085 3.055891 AGTCATCGTGGTTCACATCATCA 60.056 43.478 0.00 0.00 33.40 3.07
1065 1088 3.325870 GAAGTCATCGTGGTTCACATCA 58.674 45.455 0.00 0.00 33.40 3.07
1070 1093 1.067846 CGAGGAAGTCATCGTGGTTCA 60.068 52.381 7.18 0.00 44.02 3.18
1126 1149 8.565896 AAGTGCAGAGATGTTAATATGAAACA 57.434 30.769 6.40 6.40 40.85 2.83
1138 1161 6.455360 TTTTCTTGAAAAGTGCAGAGATGT 57.545 33.333 4.61 0.00 46.34 3.06
1141 1164 7.703621 CAGAATTTTTCTTGAAAAGTGCAGAGA 59.296 33.333 10.55 0.00 46.34 3.10
1142 1165 7.490402 ACAGAATTTTTCTTGAAAAGTGCAGAG 59.510 33.333 10.55 4.54 46.34 3.35
1190 1213 9.573133 AAACAAATCAGAACTGTTACTTTTGAG 57.427 29.630 17.25 0.00 33.05 3.02
1217 1240 2.592308 GTGCAGGCCCTCCTAAGG 59.408 66.667 0.00 0.00 41.93 2.69
1336 1359 2.167861 GTCGGCAGCGATCTGTTCC 61.168 63.158 0.00 0.00 42.29 3.62
1348 1371 1.448893 GGCGTATTTGAGGTCGGCA 60.449 57.895 0.00 0.00 45.50 5.69
1417 1440 0.386478 GCGTACCGTCTTGTTCGTCT 60.386 55.000 0.00 0.00 32.47 4.18
1437 1460 8.574737 CCTTCTCTGAACTGAATCAAAAGAATT 58.425 33.333 10.20 0.00 0.00 2.17
1440 1463 6.595682 ACCTTCTCTGAACTGAATCAAAAGA 58.404 36.000 0.00 0.00 0.00 2.52
1458 1481 5.563876 ATGATCAGCATCATGTACCTTCT 57.436 39.130 0.09 0.00 46.38 2.85
1499 1526 6.993786 TGTCTGAATTTTAACACACACAGA 57.006 33.333 0.00 0.00 0.00 3.41
1500 1527 9.385902 CTTATGTCTGAATTTTAACACACACAG 57.614 33.333 0.00 0.00 0.00 3.66
1507 1534 8.075574 CACACAGCTTATGTCTGAATTTTAACA 58.924 33.333 0.00 0.00 41.41 2.41
1508 1535 7.061094 GCACACAGCTTATGTCTGAATTTTAAC 59.939 37.037 0.00 0.00 41.41 2.01
1511 1538 5.464168 GCACACAGCTTATGTCTGAATTTT 58.536 37.500 0.00 0.00 41.41 1.82
1521 1548 1.098050 GGGAAGGCACACAGCTTATG 58.902 55.000 0.00 0.00 44.79 1.90
1551 1578 2.004489 GCGATCATCGTCGTCGTCC 61.004 63.158 9.23 0.00 42.81 4.79
1554 1581 3.085608 CCGCGATCATCGTCGTCG 61.086 66.667 8.23 9.69 42.81 5.12
1575 1602 6.373759 TGTATAATAGCTCACCTCCTCTTCA 58.626 40.000 0.00 0.00 0.00 3.02
1603 1630 5.599732 ACAAACAAGCAACTGCAAATATCA 58.400 33.333 4.22 0.00 45.16 2.15
1612 1639 3.155093 AGCTCAACAAACAAGCAACTG 57.845 42.857 0.00 0.00 38.51 3.16
1622 1649 4.393062 GCTGCAGATAACTAGCTCAACAAA 59.607 41.667 20.43 0.00 33.53 2.83
1628 1655 2.543430 GCAAGCTGCAGATAACTAGCTC 59.457 50.000 20.43 0.00 45.09 4.09
1684 1711 0.110678 CATCATCATCCTGCCCAGCT 59.889 55.000 0.00 0.00 0.00 4.24
1688 1715 1.952296 GTTGTCATCATCATCCTGCCC 59.048 52.381 0.00 0.00 0.00 5.36
1860 1890 5.514914 TCAGCAAACAAATTTTCTGACGAAC 59.485 36.000 0.00 0.00 41.35 3.95
1922 1955 0.984230 TCCACTAGTTCCTGCCCTTG 59.016 55.000 0.00 0.00 0.00 3.61
1925 1958 1.559682 TGATTCCACTAGTTCCTGCCC 59.440 52.381 0.00 0.00 0.00 5.36
1936 1969 3.588842 TCTCATTTCCCACTGATTCCACT 59.411 43.478 0.00 0.00 0.00 4.00
1972 2005 3.387374 CCAAGTATGACAGGAGCTCATCT 59.613 47.826 17.19 0.66 30.76 2.90
2037 2070 3.679389 ACTCACTCATCATGGTTTGTCC 58.321 45.455 0.00 0.00 0.00 4.02
2100 2133 6.806751 TCCAGCAATACACTAGTGATTAGTC 58.193 40.000 29.30 12.55 40.68 2.59
2102 2135 8.668510 ATTTCCAGCAATACACTAGTGATTAG 57.331 34.615 29.30 15.92 35.39 1.73
2311 2345 7.588497 AAGAAGCAATTTTTAACTCTCACCT 57.412 32.000 0.00 0.00 0.00 4.00
2387 2421 5.049198 CAGTTAATCACATGTCAGCAACTGT 60.049 40.000 21.06 1.32 37.76 3.55
2398 2432 6.502652 TGTTTCACCAACAGTTAATCACATG 58.497 36.000 0.00 0.00 40.71 3.21
2414 2449 0.890996 CTGGGCAGGTCTGTTTCACC 60.891 60.000 0.00 0.00 0.00 4.02
2595 2630 3.800261 GCCTTTTCCTTCCTTTTGACAGC 60.800 47.826 0.00 0.00 0.00 4.40
2644 2681 6.876789 TCCAACTAAATATCTGCTTTCGAACA 59.123 34.615 0.00 0.00 0.00 3.18
2649 2686 9.508567 GTGAAATCCAACTAAATATCTGCTTTC 57.491 33.333 0.00 0.00 0.00 2.62
2809 2852 5.186797 ACAAACATGACAAGGACAGGAAAAA 59.813 36.000 0.00 0.00 0.00 1.94
3017 3062 2.347731 GTAGCAGTTCAACCCTGTAGC 58.652 52.381 0.00 0.00 32.41 3.58
3037 3082 0.034059 AGAGTGTGAGTTGGCTTCGG 59.966 55.000 0.00 0.00 0.00 4.30
3039 3084 2.036475 TGAGAGAGTGTGAGTTGGCTTC 59.964 50.000 0.00 0.00 0.00 3.86
3059 3104 3.123804 CGATGAAATCTCCGGTTACCTG 58.876 50.000 0.00 0.00 42.58 4.00
3146 3191 4.326826 TGGGAAATCGCCATGAGATTATC 58.673 43.478 14.03 12.92 37.34 1.75
3235 3280 1.982938 AGAGAGCGGGCCGTTAGTT 60.983 57.895 28.82 10.77 0.00 2.24
3311 3356 3.739810 GTCGACCTAAGTTTGACTCCAAC 59.260 47.826 3.51 0.00 32.11 3.77
3334 3379 5.470098 GGAACATGTGACAGACTGTGTTATT 59.530 40.000 14.14 0.00 40.56 1.40


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

AutoCloner maintained by Alex Coulton.