Multiple sequence alignment - TraesCS7D01G222900

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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 TraesCS7D01G222900 chr7D 100.000 3324 0 0 1 3324 184188339 184185016 0.000000e+00 6139
1 TraesCS7D01G222900 chr7B 94.461 3358 115 23 4 3324 153439395 153436072 0.000000e+00 5105
2 TraesCS7D01G222900 chr7A 94.113 2633 102 27 6 2606 186530327 186532938 0.000000e+00 3954
3 TraesCS7D01G222900 chr7A 94.959 734 33 2 2594 3324 186533203 186533935 0.000000e+00 1147
4 TraesCS7D01G222900 chr4B 89.189 333 32 2 2987 3315 181507807 181508139 2.390000e-111 412
5 TraesCS7D01G222900 chr1D 88.496 339 36 1 2989 3324 197732956 197732618 1.110000e-109 407
6 TraesCS7D01G222900 chr6D 88.855 332 34 1 2987 3315 48674767 48675098 3.990000e-109 405
7 TraesCS7D01G222900 chr2D 88.788 330 33 2 2989 3315 136674717 136674389 5.170000e-108 401
8 TraesCS7D01G222900 chr1A 88.485 330 34 2 2989 3315 562082463 562082791 2.400000e-106 396
9 TraesCS7D01G222900 chr6A 88.253 332 35 2 2987 3315 65859170 65858840 8.640000e-106 394
10 TraesCS7D01G222900 chr2A 87.097 341 39 3 2978 3315 643501293 643500955 6.730000e-102 381


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 TraesCS7D01G222900 chr7D 184185016 184188339 3323 True 6139.0 6139 100.000 1 3324 1 chr7D.!!$R1 3323
1 TraesCS7D01G222900 chr7B 153436072 153439395 3323 True 5105.0 5105 94.461 4 3324 1 chr7B.!!$R1 3320
2 TraesCS7D01G222900 chr7A 186530327 186533935 3608 False 2550.5 3954 94.536 6 3324 2 chr7A.!!$F1 3318

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
343 348 0.249573 ACGGACCACAACGACGAAAT 60.250 50.000 0.00 0.0 0.0 2.17 F
344 349 0.863144 CGGACCACAACGACGAAATT 59.137 50.000 0.00 0.0 0.0 1.82 F
349 354 1.201877 CCACAACGACGAAATTAGCCG 60.202 52.381 0.00 0.0 0.0 5.52 F
927 958 1.244019 CCTGCTAGCCCAAACACACC 61.244 60.000 13.29 0.0 0.0 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1520 1557 0.117340 AAGGGGGCAGACAGAGTAGT 59.883 55.000 0.00 0.00 0.0 2.73 R
2183 2224 0.250467 TCCTGTTCCAGCTGCTCAAC 60.250 55.000 8.66 10.97 0.0 3.18 R
2245 2286 1.134401 TGCTCAGAAATAGCCCCTTCG 60.134 52.381 0.00 0.00 39.3 3.79 R
2729 3047 2.821969 GCTCTTTTTCTGCCTGATTCCA 59.178 45.455 0.00 0.00 0.0 3.53 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
22 23 1.495951 CGAGTTTACCACCGCAAGC 59.504 57.895 0.00 0.00 0.00 4.01
66 67 2.930682 GGTTCTCTCGTGGAAGCATTAC 59.069 50.000 10.78 0.00 39.88 1.89
132 134 2.543802 CGCTGATCGCCTAGGTCGA 61.544 63.158 24.04 24.04 40.45 4.20
189 191 3.003173 CTCGGAGCCCCCTCAACA 61.003 66.667 0.00 0.00 39.96 3.33
251 253 5.404946 GCACACATAATCATCAAAAGTGCT 58.595 37.500 0.00 0.00 44.49 4.40
253 255 6.034256 GCACACATAATCATCAAAAGTGCTTC 59.966 38.462 0.00 0.00 44.49 3.86
282 285 5.183904 AGTTAAACTGATTCCATGAACTGCC 59.816 40.000 0.00 0.00 0.00 4.85
285 288 4.785346 ACTGATTCCATGAACTGCCTAT 57.215 40.909 0.00 0.00 0.00 2.57
291 294 9.288576 CTGATTCCATGAACTGCCTATAAAATA 57.711 33.333 0.00 0.00 0.00 1.40
294 297 7.817418 TCCATGAACTGCCTATAAAATAACC 57.183 36.000 0.00 0.00 0.00 2.85
343 348 0.249573 ACGGACCACAACGACGAAAT 60.250 50.000 0.00 0.00 0.00 2.17
344 349 0.863144 CGGACCACAACGACGAAATT 59.137 50.000 0.00 0.00 0.00 1.82
345 350 2.060284 CGGACCACAACGACGAAATTA 58.940 47.619 0.00 0.00 0.00 1.40
346 351 2.091588 CGGACCACAACGACGAAATTAG 59.908 50.000 0.00 0.00 0.00 1.73
347 352 2.159747 GGACCACAACGACGAAATTAGC 60.160 50.000 0.00 0.00 0.00 3.09
348 353 1.802365 ACCACAACGACGAAATTAGCC 59.198 47.619 0.00 0.00 0.00 3.93
349 354 1.201877 CCACAACGACGAAATTAGCCG 60.202 52.381 0.00 0.00 0.00 5.52
350 355 1.458064 CACAACGACGAAATTAGCCGT 59.542 47.619 0.00 0.00 42.17 5.68
400 405 3.685756 GCACATACGCTTAAGTTAACCCA 59.314 43.478 4.02 0.00 0.00 4.51
513 518 2.017049 AGCAGAAAATCGTACCCATGC 58.983 47.619 0.00 0.00 0.00 4.06
537 542 1.355916 GGACCGATCGGACGAAGAG 59.644 63.158 39.55 11.67 38.96 2.85
679 708 1.682849 CATTCCCCACCTGGACGAA 59.317 57.895 0.00 0.00 37.39 3.85
709 738 2.124942 CGGCAGGAAGGAAGGAGC 60.125 66.667 0.00 0.00 0.00 4.70
717 746 2.177888 AGGAAGGAAGGAGCCAAAAGTT 59.822 45.455 0.00 0.00 0.00 2.66
728 757 2.837591 AGCCAAAAGTTCCACCAAAACT 59.162 40.909 0.00 0.00 38.59 2.66
776 805 4.598894 CAGCAGGAGATCGGGCGG 62.599 72.222 0.00 0.00 0.00 6.13
827 856 3.886505 TGTGTAATTTTGAGTTTCGGGCT 59.113 39.130 0.00 0.00 0.00 5.19
888 917 2.108776 CCCATCATAAGCCCATCCAAGA 59.891 50.000 0.00 0.00 0.00 3.02
927 958 1.244019 CCTGCTAGCCCAAACACACC 61.244 60.000 13.29 0.00 0.00 4.16
951 983 1.750022 AACCCAGTTGGCCCTAACTA 58.250 50.000 8.08 0.00 38.78 2.24
1134 1167 9.801873 ATCTTGTATTTTGGGTTTGATTTATCG 57.198 29.630 0.00 0.00 0.00 2.92
1165 1199 1.522355 CAGCGATCCTTGGATGCGT 60.522 57.895 6.92 0.00 0.00 5.24
1327 1361 4.103103 GGCTTTGCGCGGTTCTCC 62.103 66.667 8.83 0.00 40.44 3.71
1503 1540 2.561478 AAGCTCGGAAAGGTTGCTTA 57.439 45.000 0.00 0.00 43.93 3.09
1504 1541 2.561478 AGCTCGGAAAGGTTGCTTAA 57.439 45.000 0.00 0.00 29.11 1.85
1510 1547 6.015772 AGCTCGGAAAGGTTGCTTAATTTTAA 60.016 34.615 0.00 0.00 29.11 1.52
1533 1570 9.582431 TTAACATGTTATTACTACTCTGTCTGC 57.418 33.333 18.69 0.00 0.00 4.26
1534 1571 6.574350 ACATGTTATTACTACTCTGTCTGCC 58.426 40.000 0.00 0.00 0.00 4.85
1541 1578 2.225547 ACTACTCTGTCTGCCCCCTTTA 60.226 50.000 0.00 0.00 0.00 1.85
1548 1585 2.238646 TGTCTGCCCCCTTTAGTATGTG 59.761 50.000 0.00 0.00 0.00 3.21
1560 1599 6.472887 CCTTTAGTATGTGGTTGAGGAGAAA 58.527 40.000 0.00 0.00 0.00 2.52
1561 1600 7.112779 CCTTTAGTATGTGGTTGAGGAGAAAT 58.887 38.462 0.00 0.00 0.00 2.17
2164 2205 9.906660 GAGAAATATAGGTATGAACAGTCTCTG 57.093 37.037 0.00 0.00 37.52 3.35
2307 2348 3.557054 GCTGTGGATGACCTCACAACTAA 60.557 47.826 0.00 0.00 42.40 2.24
2331 2372 4.129380 TCAGATACCGATTGAATTGCCTG 58.871 43.478 0.00 0.00 0.00 4.85
2343 2384 3.778618 GAATTGCCTGCTTCCTCAATTC 58.221 45.455 9.74 9.74 43.85 2.17
2388 2429 3.006859 TGAAGGTTTGAGAAGATCTCGCA 59.993 43.478 0.00 0.00 46.25 5.10
2569 2610 4.405358 ACAAGTGTGGTGACCAATTTGATT 59.595 37.500 22.65 5.74 34.18 2.57
2654 2972 3.589951 AACATGCCCTTAGATGCAGAT 57.410 42.857 0.00 0.00 41.46 2.90
2729 3047 3.641437 TTAAACAGCGCTTCAATGCTT 57.359 38.095 7.50 0.00 40.03 3.91
2739 3057 2.737679 GCTTCAATGCTTGGAATCAGGC 60.738 50.000 0.00 0.00 44.95 4.85
3085 3406 0.517132 CGTTTCGTGAGATGCTTGCG 60.517 55.000 0.00 0.00 41.60 4.85
3139 3460 5.336213 CCATTGTTCTGTTAGATGCTTGCTT 60.336 40.000 0.00 0.00 0.00 3.91
3156 3477 7.090173 TGCTTGCTTAAAAATGTCATTAGACC 58.910 34.615 0.00 0.00 44.33 3.85
3196 3517 3.815809 ACCCGTTGACCATGTTATATGG 58.184 45.455 6.44 6.44 44.54 2.74
3227 3548 1.556911 CCTAGACCCACATGTCAGCTT 59.443 52.381 0.00 0.00 37.73 3.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.344500 CGGTGGTAAACTCGCCCA 59.656 61.111 0.00 0.00 0.00 5.36
1 2 3.122971 GCGGTGGTAAACTCGCCC 61.123 66.667 0.00 0.00 40.45 6.13
2 3 1.908066 CTTGCGGTGGTAAACTCGCC 61.908 60.000 0.00 0.00 43.52 5.54
90 91 1.640670 AGGTAATGCTGGGTTGGACAT 59.359 47.619 0.00 0.00 0.00 3.06
189 191 1.741706 CAGCAATCCATTCAGCTTCGT 59.258 47.619 0.00 0.00 34.61 3.85
282 285 6.814146 GGATCGGCTCTCAGGTTATTTTATAG 59.186 42.308 0.00 0.00 0.00 1.31
285 288 4.202326 GGGATCGGCTCTCAGGTTATTTTA 60.202 45.833 0.00 0.00 0.00 1.52
291 294 2.066999 GGGGATCGGCTCTCAGGTT 61.067 63.158 0.00 0.00 0.00 3.50
294 297 0.965439 CTTAGGGGATCGGCTCTCAG 59.035 60.000 0.00 0.00 0.00 3.35
348 353 1.154727 CTTTTCGTTTCCGCCGACG 60.155 57.895 0.00 0.00 40.43 5.12
349 354 1.205820 CCTTTTCGTTTCCGCCGAC 59.794 57.895 0.00 0.00 33.41 4.79
350 355 0.947180 CTCCTTTTCGTTTCCGCCGA 60.947 55.000 0.00 0.00 0.00 5.54
351 356 1.495951 CTCCTTTTCGTTTCCGCCG 59.504 57.895 0.00 0.00 0.00 6.46
352 357 1.583495 CCCTCCTTTTCGTTTCCGCC 61.583 60.000 0.00 0.00 0.00 6.13
353 358 1.873863 CCCTCCTTTTCGTTTCCGC 59.126 57.895 0.00 0.00 0.00 5.54
354 359 0.605589 AGCCCTCCTTTTCGTTTCCG 60.606 55.000 0.00 0.00 0.00 4.30
355 360 2.484742 TAGCCCTCCTTTTCGTTTCC 57.515 50.000 0.00 0.00 0.00 3.13
356 361 4.795268 CTTTTAGCCCTCCTTTTCGTTTC 58.205 43.478 0.00 0.00 0.00 2.78
357 362 3.005472 GCTTTTAGCCCTCCTTTTCGTTT 59.995 43.478 0.00 0.00 34.48 3.60
358 363 2.557056 GCTTTTAGCCCTCCTTTTCGTT 59.443 45.455 0.00 0.00 34.48 3.85
359 364 2.160205 GCTTTTAGCCCTCCTTTTCGT 58.840 47.619 0.00 0.00 34.48 3.85
416 421 1.042229 TTGCTCCTTGCTGCACAAAT 58.958 45.000 0.00 0.00 43.37 2.32
418 423 1.735360 GTTGCTCCTTGCTGCACAA 59.265 52.632 0.00 0.00 43.37 3.33
420 425 2.180131 CTCGTTGCTCCTTGCTGCAC 62.180 60.000 0.00 0.00 43.37 4.57
537 542 4.467084 TCGTCGCATTGCTCCCCC 62.467 66.667 7.12 0.00 0.00 5.40
709 738 3.443976 CGAGTTTTGGTGGAACTTTTGG 58.556 45.455 0.00 0.00 37.46 3.28
717 746 2.114411 GGCCCGAGTTTTGGTGGA 59.886 61.111 0.00 0.00 0.00 4.02
775 804 3.614143 GATCACGAATCGACGGCC 58.386 61.111 10.55 0.00 37.61 6.13
805 834 3.886505 AGCCCGAAACTCAAAATTACACA 59.113 39.130 0.00 0.00 0.00 3.72
888 917 1.974957 GGCCTGGTTGGTTGGTAAAAT 59.025 47.619 0.00 0.00 38.35 1.82
927 958 1.048160 AGGGCCAACTGGGTTTGTTG 61.048 55.000 6.18 0.00 42.96 3.33
1134 1167 0.107654 ATCGCTGTTAGGAGGCAACC 60.108 55.000 0.00 0.00 37.17 3.77
1165 1199 2.631580 GGGATTTGCGCCGTGGAAA 61.632 57.895 4.18 0.81 42.42 3.13
1215 1249 2.901840 CGCATCCATCAACCCCCG 60.902 66.667 0.00 0.00 0.00 5.73
1309 1343 4.445545 GAGAACCGCGCAAAGCCG 62.446 66.667 8.75 0.00 44.76 5.52
1510 1547 6.407074 GGGCAGACAGAGTAGTAATAACATGT 60.407 42.308 0.00 0.00 0.00 3.21
1519 1556 1.008403 AGGGGGCAGACAGAGTAGTA 58.992 55.000 0.00 0.00 0.00 1.82
1520 1557 0.117340 AAGGGGGCAGACAGAGTAGT 59.883 55.000 0.00 0.00 0.00 2.73
1521 1558 1.280457 AAAGGGGGCAGACAGAGTAG 58.720 55.000 0.00 0.00 0.00 2.57
1523 1560 1.280457 CTAAAGGGGGCAGACAGAGT 58.720 55.000 0.00 0.00 0.00 3.24
1524 1561 1.280457 ACTAAAGGGGGCAGACAGAG 58.720 55.000 0.00 0.00 0.00 3.35
1525 1562 2.634639 TACTAAAGGGGGCAGACAGA 57.365 50.000 0.00 0.00 0.00 3.41
1527 1564 2.238646 CACATACTAAAGGGGGCAGACA 59.761 50.000 0.00 0.00 0.00 3.41
1528 1565 2.421529 CCACATACTAAAGGGGGCAGAC 60.422 54.545 0.00 0.00 0.00 3.51
1533 1570 3.371595 CCTCAACCACATACTAAAGGGGG 60.372 52.174 0.00 0.00 0.00 5.40
1534 1571 3.521937 TCCTCAACCACATACTAAAGGGG 59.478 47.826 0.00 0.00 0.00 4.79
1541 1578 6.058183 GCATATTTCTCCTCAACCACATACT 58.942 40.000 0.00 0.00 0.00 2.12
1548 1585 6.501781 CATTTCAGCATATTTCTCCTCAACC 58.498 40.000 0.00 0.00 0.00 3.77
1560 1599 4.098807 TGACAATGCAGCATTTCAGCATAT 59.901 37.500 18.48 0.00 45.56 1.78
1561 1600 3.444388 TGACAATGCAGCATTTCAGCATA 59.556 39.130 18.48 1.60 45.56 3.14
2164 2205 6.806739 GCTCAACAAATTTACTGGTATGTTCC 59.193 38.462 0.00 0.00 0.00 3.62
2183 2224 0.250467 TCCTGTTCCAGCTGCTCAAC 60.250 55.000 8.66 10.97 0.00 3.18
2245 2286 1.134401 TGCTCAGAAATAGCCCCTTCG 60.134 52.381 0.00 0.00 39.30 3.79
2272 2313 3.049708 TCCACAGCAGAGTCTTCATTG 57.950 47.619 0.00 0.00 0.00 2.82
2307 2348 4.130118 GGCAATTCAATCGGTATCTGAGT 58.870 43.478 0.00 0.00 0.00 3.41
2331 2372 7.444792 AGAATATGAGATGTGAATTGAGGAAGC 59.555 37.037 0.00 0.00 0.00 3.86
2343 2384 4.051237 TCGCGGAAAGAATATGAGATGTG 58.949 43.478 6.13 0.00 0.00 3.21
2729 3047 2.821969 GCTCTTTTTCTGCCTGATTCCA 59.178 45.455 0.00 0.00 0.00 3.53
2739 3057 5.294306 TGAATATGCTACCGCTCTTTTTCTG 59.706 40.000 0.00 0.00 36.97 3.02
3085 3406 4.192429 AGGTGTCTAATGGCATTTTTGC 57.808 40.909 19.21 7.33 0.00 3.68
3119 3440 6.875948 TTTAAGCAAGCATCTAACAGAACA 57.124 33.333 0.00 0.00 0.00 3.18
3124 3445 7.656412 TGACATTTTTAAGCAAGCATCTAACA 58.344 30.769 0.00 0.00 0.00 2.41
3139 3460 7.334921 CAGTAACGGGGTCTAATGACATTTTTA 59.665 37.037 5.89 0.00 44.61 1.52
3156 3477 2.140717 GTTTGACCTGACAGTAACGGG 58.859 52.381 0.93 0.00 39.46 5.28
3196 3517 1.567175 TGGGTCTAGGGGTATTTTGGC 59.433 52.381 0.00 0.00 0.00 4.52
3227 3548 9.166173 CCACACTTATCATTGTGAAATAGAGAA 57.834 33.333 3.30 0.00 45.03 2.87
3261 3582 5.909621 ATTTGCTTGCTTACTCATGACAT 57.090 34.783 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.