Multiple sequence alignment - TraesCS7A01G304500

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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 TraesCS7A01G304500 chr7A 100.000 3772 0 0 1 3772 428808776 428812547 0.000000e+00 6966.0
1 TraesCS7A01G304500 chr7D 95.335 3816 105 30 1 3772 380143883 380147669 0.000000e+00 5993.0
2 TraesCS7A01G304500 chr7B 93.400 2288 76 31 1540 3772 375190718 375192985 0.000000e+00 3319.0
3 TraesCS7A01G304500 chr7B 96.212 1267 34 8 239 1495 375188986 375190248 0.000000e+00 2061.0
4 TraesCS7A01G304500 chr7B 95.522 201 6 2 1 201 375188426 375188623 6.080000e-83 318.0
5 TraesCS7A01G304500 chr5B 83.036 112 15 3 1304 1413 211146258 211146367 8.620000e-17 99.0
6 TraesCS7A01G304500 chr5A 82.883 111 17 2 1304 1413 214166634 214166743 8.620000e-17 99.0
7 TraesCS7A01G304500 chr4D 82.301 113 16 4 1312 1422 68053418 68053528 1.120000e-15 95.3
8 TraesCS7A01G304500 chr4B 81.982 111 20 0 1312 1422 100576667 100576777 1.120000e-15 95.3
9 TraesCS7A01G304500 chr4B 84.507 71 11 0 2000 2070 405906885 405906955 1.880000e-08 71.3
10 TraesCS7A01G304500 chr4A 82.301 113 16 4 1312 1422 517884598 517884708 1.120000e-15 95.3
11 TraesCS7A01G304500 chr5D 82.143 112 16 3 1304 1413 200501287 200501396 4.010000e-15 93.5
12 TraesCS7A01G304500 chr3D 94.915 59 3 0 2027 2085 253340047 253339989 4.010000e-15 93.5
13 TraesCS7A01G304500 chr3B 94.915 59 3 0 2027 2085 304277919 304277977 4.010000e-15 93.5
14 TraesCS7A01G304500 chr3B 81.308 107 18 2 1312 1417 458343140 458343245 6.710000e-13 86.1
15 TraesCS7A01G304500 chr3A 94.915 59 3 0 2027 2085 330698744 330698802 4.010000e-15 93.5
16 TraesCS7A01G304500 chr1D 88.571 70 8 0 2001 2070 8096554 8096623 6.710000e-13 86.1
17 TraesCS7A01G304500 chr1B 90.741 54 5 0 2017 2070 10569228 10569175 5.230000e-09 73.1
18 TraesCS7A01G304500 chr1A 85.714 63 9 0 2003 2065 569139252 569139190 2.430000e-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 TraesCS7A01G304500 chr7A 428808776 428812547 3771 False 6966.000000 6966 100.000000 1 3772 1 chr7A.!!$F1 3771
1 TraesCS7A01G304500 chr7D 380143883 380147669 3786 False 5993.000000 5993 95.335000 1 3772 1 chr7D.!!$F1 3771
2 TraesCS7A01G304500 chr7B 375188426 375192985 4559 False 1899.333333 3319 95.044667 1 3772 3 chr7B.!!$F1 3771

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
193 194 1.197492 CGTTGCATGCATGTGTGTACT 59.803 47.619 26.79 0.0 0.00 2.73 F
1448 1779 0.690192 TGGCAACAGGTAGCTAGCAA 59.310 50.000 24.01 0.0 46.17 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1981 2782 0.797542 GCAATACGGCCGTGTTTACA 59.202 50.0 40.02 20.46 0.00 2.41 R
3072 3886 0.179006 TACACACCAGTTGCCATGCA 60.179 50.0 0.00 0.00 36.47 3.96 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
78 79 1.425412 CCGACTACCAAACTTCACGG 58.575 55.000 0.00 0.00 0.00 4.94
125 126 5.106157 GGACAGCACCCACATATTTATATGC 60.106 44.000 9.16 0.00 42.98 3.14
160 161 2.624364 ACAACATCAACATGCAGCTCAA 59.376 40.909 0.00 0.00 32.57 3.02
161 162 3.242518 CAACATCAACATGCAGCTCAAG 58.757 45.455 0.00 0.00 32.57 3.02
193 194 1.197492 CGTTGCATGCATGTGTGTACT 59.803 47.619 26.79 0.00 0.00 2.73
314 639 8.514594 CATGTTGATTTGTCCAGTTAGTTATGT 58.485 33.333 0.00 0.00 0.00 2.29
428 755 4.715520 ACAATAGTGATTAGAATGCGCG 57.284 40.909 0.00 0.00 0.00 6.86
432 759 6.645003 ACAATAGTGATTAGAATGCGCGATTA 59.355 34.615 12.10 0.00 0.00 1.75
984 1314 4.130857 GTCACTGGTCGATCTGATCTCTA 58.869 47.826 15.16 5.99 0.00 2.43
986 1316 4.819088 TCACTGGTCGATCTGATCTCTAAG 59.181 45.833 15.16 9.93 0.00 2.18
1039 1369 1.242076 CAACCAGCAGAAGGTGAAGG 58.758 55.000 0.00 0.00 45.95 3.46
1080 1410 4.719997 GATGAGAAGCTCGTCCGG 57.280 61.111 0.00 0.00 39.75 5.14
1135 1465 3.702048 TCCCCGAGAAAGCCGGTG 61.702 66.667 1.90 0.00 45.14 4.94
1170 1500 3.214250 CTATCTCGACCGGCTGCCC 62.214 68.421 14.12 0.00 0.00 5.36
1190 1520 1.248486 CGATCCGGCCTCTCTCATTA 58.752 55.000 0.00 0.00 0.00 1.90
1217 1548 9.360093 GATTAACATATGAGTATTAGCTTCGCT 57.640 33.333 10.38 0.00 43.41 4.93
1242 1573 2.912295 TGATGACCAGTTGAAGATGGGA 59.088 45.455 1.90 0.00 41.13 4.37
1414 1745 2.548493 GGAGGAGAAGCTCATCATCAGC 60.548 54.545 12.94 0.00 42.21 4.26
1447 1778 2.371784 TGGCAACAGGTAGCTAGCA 58.628 52.632 24.01 0.00 46.17 3.49
1448 1779 0.690192 TGGCAACAGGTAGCTAGCAA 59.310 50.000 24.01 0.00 46.17 3.91
1456 1787 1.827969 AGGTAGCTAGCAAGGACACAG 59.172 52.381 24.01 0.00 0.00 3.66
1469 1804 3.421844 AGGACACAGTGGAAAATTAGCC 58.578 45.455 5.31 0.00 0.00 3.93
1476 1811 4.706962 ACAGTGGAAAATTAGCCTGATTCC 59.293 41.667 0.00 0.00 39.96 3.01
1480 1815 4.956075 TGGAAAATTAGCCTGATTCCTTCC 59.044 41.667 5.97 5.97 40.15 3.46
1488 1823 2.169144 GCCTGATTCCTTCCAATTTGGG 59.831 50.000 15.37 0.32 38.32 4.12
1534 1869 1.080569 GACAATGCCGCAACTTGGG 60.081 57.895 10.64 0.00 0.00 4.12
1553 2313 2.483876 GGCGCTGCTTATCAATCACTA 58.516 47.619 7.64 0.00 0.00 2.74
1563 2323 7.212976 TGCTTATCAATCACTAATCTGACCTC 58.787 38.462 0.00 0.00 0.00 3.85
1600 2360 8.841444 GGTGACATACAGCATTTAATTACTTG 57.159 34.615 0.00 0.00 45.12 3.16
1601 2361 8.673711 GGTGACATACAGCATTTAATTACTTGA 58.326 33.333 0.00 0.00 45.12 3.02
1602 2362 9.490663 GTGACATACAGCATTTAATTACTTGAC 57.509 33.333 0.00 0.00 0.00 3.18
1603 2363 9.448438 TGACATACAGCATTTAATTACTTGACT 57.552 29.630 0.00 0.00 0.00 3.41
1604 2364 9.708222 GACATACAGCATTTAATTACTTGACTG 57.292 33.333 12.03 12.03 0.00 3.51
1614 2374 3.423539 TTACTTGACTGCCAGCAATCT 57.576 42.857 2.53 0.00 0.00 2.40
1619 2379 3.138884 TGACTGCCAGCAATCTTGTAA 57.861 42.857 2.53 0.00 0.00 2.41
1663 2436 8.760980 TGAAATCTCCTAAAAAGAAAAGGTGA 57.239 30.769 0.00 0.00 37.33 4.02
1734 2507 4.416620 AGCGCGCTATAGCTAATTAAGAG 58.583 43.478 35.79 7.86 42.60 2.85
1735 2508 3.548268 GCGCGCTATAGCTAATTAAGAGG 59.452 47.826 26.67 4.08 39.32 3.69
1736 2509 4.106197 CGCGCTATAGCTAATTAAGAGGG 58.894 47.826 21.98 7.94 39.32 4.30
1738 2511 5.103687 GCGCTATAGCTAATTAAGAGGGTC 58.896 45.833 21.98 0.00 39.32 4.46
1740 2513 6.095160 GCGCTATAGCTAATTAAGAGGGTCTA 59.905 42.308 21.98 0.00 39.32 2.59
1741 2514 7.680113 GCGCTATAGCTAATTAAGAGGGTCTAG 60.680 44.444 21.98 1.65 39.32 2.43
1742 2515 7.337436 CGCTATAGCTAATTAAGAGGGTCTAGT 59.663 40.741 21.98 0.00 39.32 2.57
1927 2728 2.958355 TCTTCAAGGCAAAGGTTCCAAG 59.042 45.455 0.00 0.00 0.00 3.61
1959 2760 7.530426 AGCTTAGTGATGACAAAAGGAAAAT 57.470 32.000 0.94 0.00 0.00 1.82
1992 2793 4.449743 TGACTTTACTGATGTAAACACGGC 59.550 41.667 0.00 0.00 41.91 5.68
2947 3760 1.028905 TGAGGTTTTCCAAAGGTGCG 58.971 50.000 0.00 0.00 43.73 5.34
2968 3781 7.148656 GGTGCGCTTAATTTATTGTGTTTGATT 60.149 33.333 9.73 0.00 0.00 2.57
3055 3869 7.395190 TTGTAAAGAGATAACTTGCATGCAT 57.605 32.000 23.37 9.62 0.00 3.96
3056 3870 6.788243 TGTAAAGAGATAACTTGCATGCATG 58.212 36.000 26.93 26.93 0.00 4.06
3150 3964 3.010420 GGAAGGAATGAAAGGGAACTCG 58.990 50.000 0.00 0.00 42.68 4.18
3227 4041 1.620819 GCATGTCTACGGAGGGATCAT 59.379 52.381 0.00 0.00 0.00 2.45
3240 4054 4.640647 GGAGGGATCATTGTGTACCTTTTC 59.359 45.833 0.00 0.00 0.00 2.29
3376 4194 7.257722 CCCTGTCACCATACATTAACAATTTC 58.742 38.462 0.00 0.00 0.00 2.17
3395 4213 9.052759 ACAATTTCACTTTATAAACGAGTCACT 57.947 29.630 0.00 0.00 0.00 3.41
3489 4307 9.535878 CTAGACCTGGTAATAGAGATGTTTTTC 57.464 37.037 11.39 0.00 0.00 2.29
3511 4331 1.117150 TGCGGGGTGGTAATAGAGAC 58.883 55.000 0.00 0.00 0.00 3.36
3729 4549 3.774216 AGAGCAAAGATAAGAGAGGCTGT 59.226 43.478 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 5.702670 TGAATTCGATGGAATCTATCAAGCC 59.297 40.000 7.37 0.00 41.99 4.35
9 10 8.146479 TGTTGAATTCGATGGAATCTATCAAG 57.854 34.615 13.26 0.00 41.99 3.02
125 126 7.028962 TGTTGATGTTGTTGTCAAGAGAAAAG 58.971 34.615 0.00 0.00 35.22 2.27
354 679 2.028658 TGACAGTGATCTTGAGGAGTGC 60.029 50.000 0.00 0.00 0.00 4.40
355 680 3.949842 TGACAGTGATCTTGAGGAGTG 57.050 47.619 0.00 0.00 0.00 3.51
428 755 9.936759 ACCTGCTAGCTAGAGAATTATTTAATC 57.063 33.333 25.15 1.79 0.00 1.75
432 759 6.926272 CGAACCTGCTAGCTAGAGAATTATTT 59.074 38.462 25.15 5.42 0.00 1.40
984 1314 0.892358 CCATGCACACACCTCAGCTT 60.892 55.000 0.00 0.00 0.00 3.74
986 1316 2.338015 CCCATGCACACACCTCAGC 61.338 63.158 0.00 0.00 0.00 4.26
1135 1465 2.857592 TAGACGGATCAAGGTTACGC 57.142 50.000 0.00 0.00 0.00 4.42
1214 1545 1.081892 CAACTGGTCATCAAGGAGCG 58.918 55.000 0.00 0.00 38.10 5.03
1217 1548 4.566278 CCATCTTCAACTGGTCATCAAGGA 60.566 45.833 0.00 0.00 0.00 3.36
1242 1573 4.313020 AATGAATTCCAAGCCAGAGAGT 57.687 40.909 2.27 0.00 0.00 3.24
1414 1745 3.277133 CCAACAATGGCGTGGAGG 58.723 61.111 0.00 0.00 40.58 4.30
1444 1775 2.435372 TTTTCCACTGTGTCCTTGCT 57.565 45.000 7.08 0.00 0.00 3.91
1445 1776 3.733443 AATTTTCCACTGTGTCCTTGC 57.267 42.857 7.08 0.00 0.00 4.01
1446 1777 4.321230 GGCTAATTTTCCACTGTGTCCTTG 60.321 45.833 7.08 0.00 0.00 3.61
1447 1778 3.826729 GGCTAATTTTCCACTGTGTCCTT 59.173 43.478 7.08 0.00 0.00 3.36
1448 1779 3.074538 AGGCTAATTTTCCACTGTGTCCT 59.925 43.478 7.08 0.00 0.00 3.85
1456 1787 5.163509 GGAAGGAATCAGGCTAATTTTCCAC 60.164 44.000 8.41 7.05 38.63 4.02
1469 1804 2.767960 CCCCCAAATTGGAAGGAATCAG 59.232 50.000 14.62 0.00 40.96 2.90
1476 1811 4.776435 ATAATTGCCCCCAAATTGGAAG 57.224 40.909 14.62 5.23 40.96 3.46
1480 1815 6.433716 AGAACAAAATAATTGCCCCCAAATTG 59.566 34.615 0.00 0.00 34.05 2.32
1534 1869 4.450419 AGATTAGTGATTGATAAGCAGCGC 59.550 41.667 0.00 0.00 0.00 5.92
1535 1870 5.693555 TCAGATTAGTGATTGATAAGCAGCG 59.306 40.000 0.00 0.00 0.00 5.18
1553 2313 4.015084 CAAGATTTGGCAGAGGTCAGATT 58.985 43.478 0.00 0.00 0.00 2.40
1586 2346 4.800471 GCTGGCAGTCAAGTAATTAAATGC 59.200 41.667 17.16 0.00 0.00 3.56
1593 2353 3.960571 AGATTGCTGGCAGTCAAGTAAT 58.039 40.909 22.27 8.19 35.50 1.89
1596 2356 1.884579 CAAGATTGCTGGCAGTCAAGT 59.115 47.619 22.27 13.43 35.50 3.16
1597 2357 1.884579 ACAAGATTGCTGGCAGTCAAG 59.115 47.619 22.27 14.44 35.50 3.02
1600 2360 3.077359 AGTTACAAGATTGCTGGCAGTC 58.923 45.455 17.16 9.10 33.61 3.51
1601 2361 3.146104 AGTTACAAGATTGCTGGCAGT 57.854 42.857 17.16 0.00 0.00 4.40
1602 2362 5.124457 ACATTAGTTACAAGATTGCTGGCAG 59.876 40.000 10.94 10.94 0.00 4.85
1603 2363 5.009631 ACATTAGTTACAAGATTGCTGGCA 58.990 37.500 0.00 0.00 0.00 4.92
1604 2364 5.567138 ACATTAGTTACAAGATTGCTGGC 57.433 39.130 0.00 0.00 0.00 4.85
1614 2374 6.795098 AATCACTTGCGACATTAGTTACAA 57.205 33.333 0.00 0.00 0.00 2.41
1619 2379 5.940192 TTCAAATCACTTGCGACATTAGT 57.060 34.783 0.00 0.00 34.76 2.24
1658 2431 5.209818 TCGAGTAACACTTCAAATCACCT 57.790 39.130 0.00 0.00 0.00 4.00
1663 2436 5.643348 TGCATGATCGAGTAACACTTCAAAT 59.357 36.000 0.00 0.00 0.00 2.32
1734 2507 9.386010 CATATACATAGACTAGACACTAGACCC 57.614 40.741 11.94 2.50 0.00 4.46
1735 2508 8.885722 GCATATACATAGACTAGACACTAGACC 58.114 40.741 11.94 4.50 0.00 3.85
1736 2509 9.438228 TGCATATACATAGACTAGACACTAGAC 57.562 37.037 11.94 6.50 0.00 2.59
1740 2513 8.465273 TGTTGCATATACATAGACTAGACACT 57.535 34.615 0.00 0.00 0.00 3.55
1741 2514 9.347934 GATGTTGCATATACATAGACTAGACAC 57.652 37.037 2.52 0.00 36.41 3.67
1742 2515 9.077885 TGATGTTGCATATACATAGACTAGACA 57.922 33.333 2.52 0.00 36.41 3.41
1927 2728 8.425577 TTTTGTCATCACTAAGCTAGCTAATC 57.574 34.615 19.70 2.41 0.00 1.75
1959 2760 9.554395 TTACATCAGTAAAGTCATTCTGTGAAA 57.446 29.630 0.00 0.00 36.59 2.69
1981 2782 0.797542 GCAATACGGCCGTGTTTACA 59.202 50.000 40.02 20.46 0.00 2.41
1992 2793 2.828549 GGCCCACCTGCAATACGG 60.829 66.667 0.00 0.00 0.00 4.02
2342 3155 2.108514 CGGGCAGTGATGCGACATT 61.109 57.895 0.00 0.00 35.24 2.71
2614 3427 2.445654 CCTCCTCCTCCTCCAGCC 60.446 72.222 0.00 0.00 0.00 4.85
2831 3644 3.488778 ACTCTCCTTGATCATGGATGC 57.511 47.619 25.92 0.00 34.61 3.91
2847 3660 2.445525 GTGAGAGGGGGAGAGATACTCT 59.554 54.545 0.67 0.67 44.28 3.24
3072 3886 0.179006 TACACACCAGTTGCCATGCA 60.179 50.000 0.00 0.00 36.47 3.96
3150 3964 5.459536 AGAATCCAAAAGAGCAAAAGGAC 57.540 39.130 0.00 0.00 0.00 3.85
3227 4041 6.646267 AGTTAGTCACTGAAAAGGTACACAA 58.354 36.000 0.00 0.00 32.83 3.33
3489 4307 2.169769 TCTCTATTACCACCCCGCAAAG 59.830 50.000 0.00 0.00 0.00 2.77
3511 4331 5.120830 CCAATCTCTCAAGGACTGTAAAACG 59.879 44.000 0.00 0.00 0.00 3.60
3622 4442 9.573166 TGATCTCCTTTTGAAGATGAAGTTTTA 57.427 29.630 0.00 0.00 0.00 1.52


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

AutoCloner maintained by Alex Coulton.