Multiple sequence alignment - TraesCS4A01G202500

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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 TraesCS4A01G202500 chr4A 100.000 3458 0 0 1 3458 492526492 492529949 0.000000e+00 6386
1 TraesCS4A01G202500 chr4A 88.258 264 27 3 483 745 137523228 137522968 2.590000e-81 313
2 TraesCS4A01G202500 chr4A 85.551 263 28 2 487 739 685783578 685783840 2.050000e-67 267
3 TraesCS4A01G202500 chr4B 96.959 2729 60 9 751 3458 116209239 116211965 0.000000e+00 4558
4 TraesCS4A01G202500 chr4B 92.259 478 31 3 1 472 116208737 116209214 0.000000e+00 673
5 TraesCS4A01G202500 chr4D 96.544 2517 60 10 954 3458 82288392 82290893 0.000000e+00 4141
6 TraesCS4A01G202500 chr4D 91.494 964 57 7 1 940 82287218 82288180 0.000000e+00 1303
7 TraesCS4A01G202500 chr3D 87.778 270 23 4 486 745 24569711 24569442 1.210000e-79 307
8 TraesCS4A01G202500 chr3B 87.361 269 24 5 487 745 534159664 534159396 2.020000e-77 300
9 TraesCS4A01G202500 chr3B 86.989 269 25 4 487 745 463484170 463483902 9.390000e-76 294
10 TraesCS4A01G202500 chr5B 87.452 263 23 4 487 739 710235624 710235886 9.390000e-76 294
11 TraesCS4A01G202500 chr5B 88.060 67 2 3 691 751 7351311 7351377 1.330000e-09 75
12 TraesCS4A01G202500 chr2B 86.617 269 26 2 487 745 795075206 795074938 4.370000e-74 289
13 TraesCS4A01G202500 chr7B 86.692 263 25 4 487 739 648273506 648273768 2.030000e-72 283
14 TraesCS4A01G202500 chr7A 86.770 257 31 2 489 742 80569082 80568826 2.030000e-72 283
15 TraesCS4A01G202500 chr7A 85.765 281 24 8 486 751 154391524 154391245 2.030000e-72 283
16 TraesCS4A01G202500 chr3A 84.528 265 28 4 488 742 688007105 688007366 2.060000e-62 250
17 TraesCS4A01G202500 chr2A 80.919 283 36 7 487 751 55953340 55953058 1.260000e-49 207
18 TraesCS4A01G202500 chr2A 79.078 282 39 9 489 751 748216155 748215875 3.550000e-40 176


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 TraesCS4A01G202500 chr4A 492526492 492529949 3457 False 6386.0 6386 100.000 1 3458 1 chr4A.!!$F1 3457
1 TraesCS4A01G202500 chr4B 116208737 116211965 3228 False 2615.5 4558 94.609 1 3458 2 chr4B.!!$F1 3457
2 TraesCS4A01G202500 chr4D 82287218 82290893 3675 False 2722.0 4141 94.019 1 3458 2 chr4D.!!$F1 3457

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
159 165 0.038744 CCTGCCAAATCACCTCCAGT 59.961 55.0 0.00 0.0 0.0 4.00 F
603 620 0.386858 GCGACGACTACAAGCACTGA 60.387 55.0 0.00 0.0 0.0 3.41 F
715 740 0.602638 TAACCAGCGCACCAGAACAG 60.603 55.0 11.47 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1419 1665 0.179059 TGTCAAGAAGTGCGCTGGAA 60.179 50.0 9.73 0.0 0.0 3.53 R
1470 1716 0.536687 TCTCGTCGAACACCCTCACT 60.537 55.0 0.00 0.0 0.0 3.41 R
2696 2943 0.394352 ACCCAATCACCGCTTCATCC 60.394 55.0 0.00 0.0 0.0 3.51 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
27 32 8.855110 CCCTTAGGTGCACTAGATATAGATATG 58.145 40.741 17.98 0.00 32.16 1.78
48 53 0.404040 AGGAACCAAAGCCGAATCCA 59.596 50.000 0.00 0.00 0.00 3.41
53 58 1.000896 CAAAGCCGAATCCACCCCT 60.001 57.895 0.00 0.00 0.00 4.79
159 165 0.038744 CCTGCCAAATCACCTCCAGT 59.961 55.000 0.00 0.00 0.00 4.00
182 188 3.117888 AGTTGGCTTCCACCGATGAATAT 60.118 43.478 0.00 0.00 30.78 1.28
204 210 3.138468 TGACCGATAGAAGAGATGGGAGA 59.862 47.826 0.00 0.00 39.76 3.71
408 414 4.406972 TGAGAACCATGTCTGCTATTAGCT 59.593 41.667 16.29 0.00 42.97 3.32
581 598 4.667519 ACATCTAGGTCCGTAAATCACC 57.332 45.455 0.00 0.00 0.00 4.02
603 620 0.386858 GCGACGACTACAAGCACTGA 60.387 55.000 0.00 0.00 0.00 3.41
607 624 0.710567 CGACTACAAGCACTGAAGCG 59.289 55.000 0.00 0.00 40.15 4.68
609 626 2.611518 GACTACAAGCACTGAAGCGAT 58.388 47.619 0.00 0.00 40.15 4.58
610 627 2.996621 GACTACAAGCACTGAAGCGATT 59.003 45.455 0.00 0.00 40.15 3.34
638 655 4.473520 CCGCTGTCATCGGCCCTT 62.474 66.667 1.54 0.00 42.47 3.95
640 657 2.268920 GCTGTCATCGGCCCTTCA 59.731 61.111 0.00 0.00 39.82 3.02
650 667 2.586357 GCCCTTCATCGTCGGAGC 60.586 66.667 0.00 0.00 0.00 4.70
652 669 2.278857 CCTTCATCGTCGGAGCCG 60.279 66.667 1.74 1.74 41.35 5.52
653 670 2.278857 CTTCATCGTCGGAGCCGG 60.279 66.667 9.29 0.00 40.25 6.13
654 671 2.752640 TTCATCGTCGGAGCCGGA 60.753 61.111 5.05 0.00 40.25 5.14
659 676 1.956629 ATCGTCGGAGCCGGACAAAT 61.957 55.000 5.05 1.14 40.25 2.32
674 691 6.238022 GCCGGACAAATATTGTTGTAGTAGAC 60.238 42.308 5.05 0.00 45.52 2.59
680 697 7.544566 ACAAATATTGTTGTAGTAGACAGTCGG 59.455 37.037 0.00 0.00 42.22 4.79
681 698 3.928727 TTGTTGTAGTAGACAGTCGGG 57.071 47.619 0.00 0.00 39.88 5.14
687 704 1.451067 AGTAGACAGTCGGGAAGTCG 58.549 55.000 0.00 0.00 37.36 4.18
705 730 2.171725 GTCGTCCCATAACCAGCGC 61.172 63.158 0.00 0.00 0.00 5.92
709 734 2.045438 CCCATAACCAGCGCACCA 60.045 61.111 11.47 0.00 0.00 4.17
710 735 2.114670 CCCATAACCAGCGCACCAG 61.115 63.158 11.47 0.00 0.00 4.00
715 740 0.602638 TAACCAGCGCACCAGAACAG 60.603 55.000 11.47 0.00 0.00 3.16
733 758 3.427425 CAACCGCCGCCGATGAAA 61.427 61.111 0.00 0.00 36.29 2.69
753 782 5.880332 TGAAAAGAAGTATCGAAAGGATGGG 59.120 40.000 0.00 0.00 36.55 4.00
780 809 3.559069 CCTGGAGGCATTATGTGTTGAT 58.441 45.455 0.00 0.00 0.00 2.57
841 871 6.424812 GGACTTTAGTTAGTAAAAACGCCTGA 59.575 38.462 0.00 0.00 34.46 3.86
911 952 1.271840 ATAGAAGCCTTGCCCGACCA 61.272 55.000 0.00 0.00 0.00 4.02
1264 1510 1.051556 CCCACCCCTCTTAGCTCTCC 61.052 65.000 0.00 0.00 0.00 3.71
1419 1665 6.310149 AGGATTTCTCTCCAATCTTGTTGTT 58.690 36.000 0.00 0.00 37.81 2.83
1470 1716 0.325933 CTGGTCTCCTGGTCAATGCA 59.674 55.000 0.00 0.00 0.00 3.96
1494 1740 1.080093 GGTGTTCGACGAGATGCCA 60.080 57.895 0.00 0.00 0.00 4.92
1527 1773 3.225940 TGTTGTGTGGAATTGCATGGTA 58.774 40.909 1.94 0.00 0.00 3.25
1530 1776 3.495331 TGTGTGGAATTGCATGGTAACT 58.505 40.909 1.94 0.00 37.61 2.24
1977 2223 1.214062 CTCAGGGCTCGTGACTGAC 59.786 63.158 7.83 0.00 36.41 3.51
2696 2943 3.049708 TCTGAACCAAGATGCTGTGAG 57.950 47.619 0.00 0.00 0.00 3.51
2750 2997 2.737252 GTTCTTCAGTTTGAGGCTACGG 59.263 50.000 0.00 0.00 0.00 4.02
3191 3447 5.244851 TGGCCATTTTAATCAAGCTGTAACA 59.755 36.000 0.00 0.00 0.00 2.41
3236 3492 1.001181 CCATGAGTTTTTGTGCCTGGG 59.999 52.381 0.00 0.00 0.00 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 32 1.472878 GGATTCGGCTTTGGTTCCTTC 59.527 52.381 0.00 0.00 0.00 3.46
48 53 0.547954 GGTGGAAGGAGAGAAGGGGT 60.548 60.000 0.00 0.00 0.00 4.95
53 58 1.132849 TGTGGAGGTGGAAGGAGAGAA 60.133 52.381 0.00 0.00 0.00 2.87
95 100 4.202284 GGTGGGCTAGAACGGTTTGATATA 60.202 45.833 0.00 0.00 0.00 0.86
96 101 3.433173 GGTGGGCTAGAACGGTTTGATAT 60.433 47.826 0.00 0.00 0.00 1.63
159 165 1.271856 TCATCGGTGGAAGCCAACTA 58.728 50.000 0.00 0.00 39.46 2.24
182 188 3.138468 TCTCCCATCTCTTCTATCGGTCA 59.862 47.826 0.00 0.00 0.00 4.02
204 210 2.268076 GCAGGTTGCGTCCAATGGT 61.268 57.895 0.00 0.00 31.71 3.55
408 414 7.775053 AGACAAGCCTTGAAATAACCAAATA 57.225 32.000 12.25 0.00 0.00 1.40
507 524 5.013079 ACCTTGACAGTTGATGAATAGACCA 59.987 40.000 0.00 0.00 0.00 4.02
509 526 7.324178 ACTACCTTGACAGTTGATGAATAGAC 58.676 38.462 0.00 0.00 0.00 2.59
577 594 1.736126 CTTGTAGTCGTCGCTAGGTGA 59.264 52.381 0.00 0.00 0.00 4.02
581 598 1.130749 AGTGCTTGTAGTCGTCGCTAG 59.869 52.381 0.00 0.00 0.00 3.42
603 620 3.554692 CGCGCCTTCGAATCGCTT 61.555 61.111 29.19 0.00 45.87 4.68
625 642 1.143838 CGATGAAGGGCCGATGACA 59.856 57.895 0.00 0.00 0.00 3.58
633 650 2.586357 GCTCCGACGATGAAGGGC 60.586 66.667 0.00 0.00 0.00 5.19
638 655 3.515286 GTCCGGCTCCGACGATGA 61.515 66.667 10.28 0.00 42.83 2.92
640 657 1.956629 ATTTGTCCGGCTCCGACGAT 61.957 55.000 10.28 2.82 42.83 3.73
650 667 6.814644 TGTCTACTACAACAATATTTGTCCGG 59.185 38.462 0.00 0.00 44.59 5.14
652 669 8.773404 ACTGTCTACTACAACAATATTTGTCC 57.227 34.615 0.00 0.00 44.59 4.02
653 670 8.584600 CGACTGTCTACTACAACAATATTTGTC 58.415 37.037 6.21 0.00 44.59 3.18
659 676 5.255687 TCCCGACTGTCTACTACAACAATA 58.744 41.667 6.21 0.00 37.74 1.90
674 691 1.154263 GACGACGACTTCCCGACTG 60.154 63.158 0.00 0.00 0.00 3.51
680 697 1.470458 GGTTATGGGACGACGACTTCC 60.470 57.143 0.00 1.79 34.26 3.46
681 698 1.203052 TGGTTATGGGACGACGACTTC 59.797 52.381 0.00 0.00 0.00 3.01
687 704 2.171725 GCGCTGGTTATGGGACGAC 61.172 63.158 0.00 0.00 0.00 4.34
705 730 2.639286 GCGGTTGCTGTTCTGGTG 59.361 61.111 0.00 0.00 38.39 4.17
726 751 6.887376 TCCTTTCGATACTTCTTTTCATCG 57.113 37.500 0.00 0.00 41.17 3.84
727 752 7.254932 CCCATCCTTTCGATACTTCTTTTCATC 60.255 40.741 0.00 0.00 0.00 2.92
733 758 4.225267 ACACCCATCCTTTCGATACTTCTT 59.775 41.667 0.00 0.00 0.00 2.52
753 782 2.172717 ACATAATGCCTCCAGGGTACAC 59.827 50.000 0.00 0.00 37.43 2.90
780 809 1.774110 ATTGGCCATTACCGATTGCA 58.226 45.000 6.09 0.00 28.53 4.08
841 871 7.307692 GGTTTTCACCGATTTATGTGCAATTTT 60.308 33.333 0.00 0.00 31.60 1.82
876 907 2.901051 CTATGCGTCCGGCTCCGTTT 62.901 60.000 7.59 0.00 44.05 3.60
911 952 2.936912 GCCTCACTCACGAGCAGGT 61.937 63.158 12.19 0.00 35.34 4.00
965 1211 1.532868 GCTTTGAGGTGTACAGTGCTG 59.467 52.381 0.00 0.00 0.00 4.41
1264 1510 1.754226 GAGGAGGCCAGAGAGTAGTTG 59.246 57.143 5.01 0.00 0.00 3.16
1348 1594 4.722700 GCCAAGAAGCGGCTCCCA 62.723 66.667 1.45 0.00 46.56 4.37
1368 1614 1.280710 ACGGTAAATCCATGGAGTGCA 59.719 47.619 21.33 6.62 35.57 4.57
1392 1638 8.112183 ACAACAAGATTGGAGAGAAATCCTAAT 58.888 33.333 0.00 0.00 40.29 1.73
1411 1657 0.381801 AGTGCGCTGGAAACAACAAG 59.618 50.000 9.73 0.00 42.06 3.16
1419 1665 0.179059 TGTCAAGAAGTGCGCTGGAA 60.179 50.000 9.73 0.00 0.00 3.53
1470 1716 0.536687 TCTCGTCGAACACCCTCACT 60.537 55.000 0.00 0.00 0.00 3.41
1494 1740 3.706594 TCCACACAACAGAGTCTCTTTCT 59.293 43.478 0.00 0.00 0.00 2.52
1977 2223 1.372251 CTCGAAGATCATCCGGCCG 60.372 63.158 21.04 21.04 33.89 6.13
2221 2467 8.243961 AGAGTGATATAGTTACTGACATTGCT 57.756 34.615 0.00 0.00 0.00 3.91
2585 2832 4.959596 ATTGCTCATGTGAACTCATGAC 57.040 40.909 13.21 11.27 45.89 3.06
2696 2943 0.394352 ACCCAATCACCGCTTCATCC 60.394 55.000 0.00 0.00 0.00 3.51
2750 2997 1.000731 AGTCACTTCAGAGCAGACAGC 59.999 52.381 0.00 0.00 46.19 4.40
3191 3447 5.485353 TGACTGTACCAATCTCTTTCTGGAT 59.515 40.000 0.00 0.00 34.16 3.41
3216 3472 1.001181 CCCAGGCACAAAAACTCATGG 59.999 52.381 0.00 0.00 0.00 3.66
3257 3513 7.918562 GCAAAAGAACCACTGATTAGTTTACAA 59.081 33.333 0.00 0.00 34.07 2.41
3263 3519 7.173390 GTCTAAGCAAAAGAACCACTGATTAGT 59.827 37.037 6.01 0.00 38.37 2.24


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

AutoCloner maintained by Alex Coulton.