Multiple sequence alignment - TraesCS7D01G526700

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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 TraesCS7D01G526700 chr7D 100.000 4368 0 0 1 4368 621984883 621989250 0.000000e+00 8067.0
1 TraesCS7D01G526700 chr7D 79.332 808 130 29 2043 2828 622165308 622166100 2.310000e-147 532.0
2 TraesCS7D01G526700 chr7D 78.462 520 88 13 1012 1517 622164487 622164996 7.050000e-83 318.0
3 TraesCS7D01G526700 chr7D 88.806 134 15 0 4 137 484413730 484413597 9.720000e-37 165.0
4 TraesCS7D01G526700 chr7B 97.442 4378 97 5 1 4368 717559975 717555603 0.000000e+00 7450.0
5 TraesCS7D01G526700 chr7B 78.961 789 140 20 2031 2808 717282162 717282935 8.380000e-142 514.0
6 TraesCS7D01G526700 chr7B 79.045 754 132 17 2047 2792 717175367 717176102 1.090000e-135 494.0
7 TraesCS7D01G526700 chr7B 79.045 754 132 17 2047 2792 717250020 717250755 1.090000e-135 494.0
8 TraesCS7D01G526700 chr7B 80.808 495 84 7 1024 1510 720059215 720059706 1.150000e-100 377.0
9 TraesCS7D01G526700 chr7B 78.439 538 109 6 2044 2577 720060117 720060651 1.160000e-90 344.0
10 TraesCS7D01G526700 chr6A 80.621 805 128 20 2044 2832 1879223 1878431 8.090000e-167 597.0
11 TraesCS7D01G526700 chr6B 78.865 828 138 27 2029 2832 726907 726093 3.870000e-145 525.0
12 TraesCS7D01G526700 chr6B 85.915 71 6 1 1718 1788 606964658 606964592 6.060000e-09 73.1
13 TraesCS7D01G526700 chr6D 78.208 826 140 28 2029 2832 2880560 2879753 3.930000e-135 492.0
14 TraesCS7D01G526700 chr6D 88.321 137 16 0 3 139 167312950 167313086 9.720000e-37 165.0
15 TraesCS7D01G526700 chr7A 77.479 817 150 26 2081 2888 717812959 717813750 3.980000e-125 459.0
16 TraesCS7D01G526700 chr4A 88.889 135 15 0 3 137 743396469 743396603 2.700000e-37 167.0
17 TraesCS7D01G526700 chr4A 93.878 49 3 0 1743 1791 148132993 148133041 1.680000e-09 75.0
18 TraesCS7D01G526700 chr3D 87.857 140 16 1 4 142 104811313 104811452 3.500000e-36 163.0
19 TraesCS7D01G526700 chr2B 88.235 136 16 0 2 137 41130969 41131104 3.500000e-36 163.0
20 TraesCS7D01G526700 chr2B 95.455 44 2 0 1745 1788 655839618 655839661 2.180000e-08 71.3
21 TraesCS7D01G526700 chr2A 88.235 136 16 0 2 137 82046090 82046225 3.500000e-36 163.0
22 TraesCS7D01G526700 chr2A 84.091 88 10 2 1705 1788 115452806 115452893 1.010000e-11 82.4
23 TraesCS7D01G526700 chr3B 88.235 136 15 1 4 139 95459110 95458976 1.260000e-35 161.0
24 TraesCS7D01G526700 chr2D 86.765 136 16 2 8 142 311569714 311569848 2.720000e-32 150.0
25 TraesCS7D01G526700 chr1A 85.227 88 12 1 1702 1788 568396074 568396161 6.020000e-14 89.8
26 TraesCS7D01G526700 chr5A 84.706 85 12 1 1705 1788 624795511 624795595 2.800000e-12 84.2
27 TraesCS7D01G526700 chr4D 93.878 49 3 0 1743 1791 323574881 323574833 1.680000e-09 75.0
28 TraesCS7D01G526700 chr5D 93.750 48 1 2 1748 1793 449030546 449030499 2.180000e-08 71.3


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 TraesCS7D01G526700 chr7D 621984883 621989250 4367 False 8067.0 8067 100.0000 1 4368 1 chr7D.!!$F1 4367
1 TraesCS7D01G526700 chr7D 622164487 622166100 1613 False 425.0 532 78.8970 1012 2828 2 chr7D.!!$F2 1816
2 TraesCS7D01G526700 chr7B 717555603 717559975 4372 True 7450.0 7450 97.4420 1 4368 1 chr7B.!!$R1 4367
3 TraesCS7D01G526700 chr7B 717282162 717282935 773 False 514.0 514 78.9610 2031 2808 1 chr7B.!!$F3 777
4 TraesCS7D01G526700 chr7B 717175367 717176102 735 False 494.0 494 79.0450 2047 2792 1 chr7B.!!$F1 745
5 TraesCS7D01G526700 chr7B 717250020 717250755 735 False 494.0 494 79.0450 2047 2792 1 chr7B.!!$F2 745
6 TraesCS7D01G526700 chr7B 720059215 720060651 1436 False 360.5 377 79.6235 1024 2577 2 chr7B.!!$F4 1553
7 TraesCS7D01G526700 chr6A 1878431 1879223 792 True 597.0 597 80.6210 2044 2832 1 chr6A.!!$R1 788
8 TraesCS7D01G526700 chr6B 726093 726907 814 True 525.0 525 78.8650 2029 2832 1 chr6B.!!$R1 803
9 TraesCS7D01G526700 chr6D 2879753 2880560 807 True 492.0 492 78.2080 2029 2832 1 chr6D.!!$R1 803
10 TraesCS7D01G526700 chr7A 717812959 717813750 791 False 459.0 459 77.4790 2081 2888 1 chr7A.!!$F1 807

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
206 207 0.110373 GGCCGTGTGTCGTGAAATTC 60.110 55.000 0.00 0.00 37.94 2.17 F
267 268 1.002134 AATGGCCTCCAGTCCAACG 60.002 57.895 3.32 0.00 36.75 4.10 F
367 368 1.650528 AGGGGGTCAAGAGACTTCAG 58.349 55.000 0.00 0.00 44.36 3.02 F
1020 1021 1.783284 TGCAGAGAACACGTGATGAC 58.217 50.000 25.01 10.68 0.00 3.06 F
2673 2963 3.417069 AGATTCACATCCACACCGAAA 57.583 42.857 0.00 0.00 0.00 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2008 2256 4.335400 TTCTCAGCACATGTACACTTCA 57.665 40.909 0.00 0.0 0.0 3.02 R
2384 2656 5.373222 TGGTGCCATATATCCACTACAAAC 58.627 41.667 11.03 0.0 0.0 2.93 R
2673 2963 7.145323 GGTGCGCATATTTTTCCTTTGTATAT 58.855 34.615 15.91 0.0 0.0 0.86 R
2957 3256 2.290367 TGTCAGACCTGTTGATTTTGCG 59.710 45.455 0.00 0.0 0.0 4.85 R
3627 3926 4.439305 TGTGCAAGCCAATCTAATCAAC 57.561 40.909 0.00 0.0 0.0 3.18 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
130 131 4.034510 GCAGACCAATAAATCAGGACGAAG 59.965 45.833 0.00 0.00 0.00 3.79
172 173 4.127171 GGATGAGGCACGTGTTAATGTAT 58.873 43.478 18.38 3.17 0.00 2.29
198 199 1.809619 CACCTATGGCCGTGTGTCG 60.810 63.158 8.05 0.00 39.52 4.35
206 207 0.110373 GGCCGTGTGTCGTGAAATTC 60.110 55.000 0.00 0.00 37.94 2.17
267 268 1.002134 AATGGCCTCCAGTCCAACG 60.002 57.895 3.32 0.00 36.75 4.10
367 368 1.650528 AGGGGGTCAAGAGACTTCAG 58.349 55.000 0.00 0.00 44.36 3.02
478 479 2.616960 TCTGCAGCCTAAACACATACG 58.383 47.619 9.47 0.00 0.00 3.06
481 482 3.142951 TGCAGCCTAAACACATACGTTT 58.857 40.909 0.00 0.00 41.78 3.60
516 517 9.781834 ATATTTATGAAAACCACATGTACAACG 57.218 29.630 0.00 0.00 0.00 4.10
615 616 9.226606 TCTGGAACCAAAAGTAGTATACAAATG 57.773 33.333 5.50 0.00 46.26 2.32
753 754 1.800586 CACAGTCATCACACCCTTTCG 59.199 52.381 0.00 0.00 0.00 3.46
763 764 3.839490 TCACACCCTTTCGTATTCCCTTA 59.161 43.478 0.00 0.00 0.00 2.69
820 821 7.234371 TCAAATTGGTGAAATGGAACCATTCTA 59.766 33.333 17.70 8.56 45.66 2.10
830 831 5.799827 TGGAACCATTCTAAAAACTTGGG 57.200 39.130 0.00 0.00 0.00 4.12
955 956 2.527497 TGGTGCCATCACAAACATCAT 58.473 42.857 0.00 0.00 44.87 2.45
963 964 7.958567 GTGCCATCACAAACATCATTATTTTTG 59.041 33.333 0.00 0.00 42.66 2.44
1020 1021 1.783284 TGCAGAGAACACGTGATGAC 58.217 50.000 25.01 10.68 0.00 3.06
1537 1564 5.751243 ACTGAACACAATACTGTTGAACC 57.249 39.130 0.00 0.00 34.40 3.62
1638 1851 8.628630 TCCATAAAGACACAAATACACATCAA 57.371 30.769 0.00 0.00 0.00 2.57
1711 1924 8.589338 CCACTGGCATAATAGAATCTACTACTT 58.411 37.037 0.00 0.00 0.00 2.24
1865 2111 8.745590 GTTACAGGAAAATTAGGCATCCTTTTA 58.254 33.333 0.00 0.00 40.29 1.52
1866 2112 7.978099 ACAGGAAAATTAGGCATCCTTTTAT 57.022 32.000 0.00 0.00 40.29 1.40
1883 2129 6.777091 TCCTTTTATATGGCATGCTGTACAAT 59.223 34.615 18.92 5.79 0.00 2.71
2008 2256 5.948742 ACTAGGTTCCTCGTACTAGTAGT 57.051 43.478 8.14 8.14 43.00 2.73
2021 2269 6.875726 TCGTACTAGTAGTGAAGTGTACATGT 59.124 38.462 13.29 2.69 32.41 3.21
2673 2963 3.417069 AGATTCACATCCACACCGAAA 57.583 42.857 0.00 0.00 0.00 3.46
2901 3199 8.218488 ACAGTCCTAGTATGTCTACATATGTCA 58.782 37.037 12.68 4.82 40.53 3.58
2957 3256 6.935167 AGTGAATCAACCCAAATTTACCATC 58.065 36.000 0.00 0.00 0.00 3.51
3089 3388 5.297547 CACTAAACACTACTGGAAGCAAGA 58.702 41.667 0.00 0.00 37.60 3.02
3091 3390 5.758784 ACTAAACACTACTGGAAGCAAGAAC 59.241 40.000 0.00 0.00 37.60 3.01
3219 3518 1.941209 GCCGAGCACAATCAGACAGAA 60.941 52.381 0.00 0.00 0.00 3.02
3268 3567 0.671781 AGCGACAATCAGCCACTGAC 60.672 55.000 0.00 0.00 43.63 3.51
3392 3691 9.499479 AGGATGACAACATATGATCTTACATTC 57.501 33.333 10.38 6.22 36.82 2.67
3428 3727 8.560576 AATGAAACGGAATTAATTATTGAGCG 57.439 30.769 0.00 0.00 0.00 5.03
3434 3733 6.481976 ACGGAATTAATTATTGAGCGATGACA 59.518 34.615 0.00 0.00 0.00 3.58
3448 3747 3.983344 GCGATGACAAATATGATTTGCCC 59.017 43.478 11.00 5.31 32.93 5.36
3486 3785 3.777106 AAATGACAGTCTCTTGCTCCA 57.223 42.857 1.31 0.00 0.00 3.86
3514 3813 9.935241 AACATAATGCACCATGTTTTATGTTTA 57.065 25.926 19.39 0.00 44.71 2.01
3542 3841 8.683615 TCAGGACAAATACACTACTACTATGTG 58.316 37.037 0.00 0.00 37.67 3.21
3593 3892 9.458374 CACAAATAATTACTTTGAGGTTTCGTT 57.542 29.630 18.84 0.00 37.12 3.85
3646 3945 7.408756 AATTAGTTGATTAGATTGGCTTGCA 57.591 32.000 0.00 0.00 0.00 4.08
3772 4071 8.608844 TTTGTTTGTTGACAAGTTTAACCAAT 57.391 26.923 0.00 0.00 40.33 3.16
3803 4102 6.646653 AGAAAACTTATTTGCAAAAGCTAGGC 59.353 34.615 17.19 3.11 0.00 3.93
3847 4146 8.177663 AGTATAAATGAAACTTGTGATTGCTCG 58.822 33.333 0.00 0.00 0.00 5.03
3958 4257 3.618690 ACAAGGCATTAGAGGTCTGAC 57.381 47.619 0.00 0.00 0.00 3.51
3970 4269 8.660373 CATTAGAGGTCTGACATTTTGAGTAAC 58.340 37.037 10.38 0.00 0.00 2.50
4000 4299 4.337304 TCAGCTGGGAGCCTGGGA 62.337 66.667 15.13 0.00 43.77 4.37
4046 4345 5.053978 AGAGTTTCATCCTTGTTTGACCT 57.946 39.130 0.00 0.00 0.00 3.85
4094 4393 7.147312 CACCAGAAAGAAAGCATTTGATTGTA 58.853 34.615 0.00 0.00 39.27 2.41
4121 4420 6.161855 TGTTGTGAGTCTATGACTTCACTT 57.838 37.500 19.92 0.00 43.53 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
80 81 7.992754 ATTATTTTGTGCCAAATTTTAGCCA 57.007 28.000 7.35 3.35 0.00 4.75
130 131 1.648504 GGCACAACCACGGTACTATC 58.351 55.000 0.00 0.00 38.86 2.08
198 199 4.019174 ACCCATCTGACATGGAATTTCAC 58.981 43.478 1.96 0.00 41.64 3.18
206 207 0.750546 CTGGCACCCATCTGACATGG 60.751 60.000 0.00 0.00 38.88 3.66
267 268 1.118356 TTTTGCCCCCACATGTCACC 61.118 55.000 0.00 0.00 0.00 4.02
367 368 6.406961 GGAAAATAAAGATCACCCCCATCAAC 60.407 42.308 0.00 0.00 0.00 3.18
516 517 1.457346 CCAGCTGGATGGTTGTCTTC 58.543 55.000 29.88 0.00 37.39 2.87
753 754 7.541122 CAACTAACTTGCTCTAAGGGAATAC 57.459 40.000 0.00 0.00 40.84 1.89
830 831 6.574350 AGACCACTATGTGTATTACTTGCTC 58.426 40.000 0.00 0.00 0.00 4.26
988 989 3.851458 TCTCTGCATACCTGATTGCAT 57.149 42.857 0.00 0.00 46.87 3.96
1020 1021 4.686191 ATCATGTAGCTTCTTCTCCAGG 57.314 45.455 0.00 0.00 0.00 4.45
1483 1506 5.116180 CAGAAATATGGTTGTCGAGGCTTA 58.884 41.667 0.00 0.00 0.00 3.09
1638 1851 9.593565 TGTATCTGTGTCCAAAGATATAGAGAT 57.406 33.333 9.77 0.00 35.40 2.75
1730 1943 6.016860 AGGTTACTACTTTTTGCCCTAAAACG 60.017 38.462 0.00 0.00 37.96 3.60
1780 1993 7.287927 GGCTATAGCAGTTGATATATACTCCCA 59.712 40.741 25.53 0.00 44.36 4.37
1865 2111 6.720112 AGAAAATTGTACAGCATGCCATAT 57.280 33.333 15.66 0.00 42.53 1.78
1866 2112 6.528537 AAGAAAATTGTACAGCATGCCATA 57.471 33.333 15.66 4.00 42.53 2.74
2008 2256 4.335400 TTCTCAGCACATGTACACTTCA 57.665 40.909 0.00 0.00 0.00 3.02
2382 2654 5.470098 GGTGCCATATATCCACTACAAACTG 59.530 44.000 11.03 0.00 0.00 3.16
2384 2656 5.373222 TGGTGCCATATATCCACTACAAAC 58.627 41.667 11.03 0.00 0.00 2.93
2673 2963 7.145323 GGTGCGCATATTTTTCCTTTGTATAT 58.855 34.615 15.91 0.00 0.00 0.86
2867 3164 4.883083 ACATACTAGGACTGTTGTGTGTG 58.117 43.478 0.00 0.00 34.42 3.82
2901 3199 7.914427 AAAAGGAAAAAGGAACATTAGGACT 57.086 32.000 0.00 0.00 0.00 3.85
2957 3256 2.290367 TGTCAGACCTGTTGATTTTGCG 59.710 45.455 0.00 0.00 0.00 4.85
3219 3518 5.975988 TGCCTTTACTCCCTCTTGATAAT 57.024 39.130 0.00 0.00 0.00 1.28
3268 3567 2.353208 GGTGCTTACCTCAGACTCAGTG 60.353 54.545 0.00 0.00 0.00 3.66
3343 3642 8.296713 TCCTAAATTGCACAATACAAGACTTTC 58.703 33.333 0.00 0.00 0.00 2.62
3386 3685 8.402472 CCGTTTCATTAGCCAAAATAGAATGTA 58.598 33.333 0.00 0.00 0.00 2.29
3392 3691 9.796120 TTAATTCCGTTTCATTAGCCAAAATAG 57.204 29.630 0.00 0.00 0.00 1.73
3399 3698 9.959749 TCAATAATTAATTCCGTTTCATTAGCC 57.040 29.630 3.39 0.00 0.00 3.93
3428 3727 5.302568 TCCTGGGCAAATCATATTTGTCATC 59.697 40.000 16.29 3.67 35.85 2.92
3434 3733 6.408869 CAAACTTCCTGGGCAAATCATATTT 58.591 36.000 0.00 0.00 0.00 1.40
3448 3747 8.885494 TGTCATTTTTATTTCCAAACTTCCTG 57.115 30.769 0.00 0.00 0.00 3.86
3514 3813 8.904834 CATAGTAGTAGTGTATTTGTCCTGACT 58.095 37.037 0.00 0.00 0.00 3.41
3542 3841 9.535878 TGGTTATGATTTTAAACCACAAAAGTC 57.464 29.630 2.13 0.00 45.85 3.01
3585 3884 5.184287 TCTCCCCAATTTCATTAACGAAACC 59.816 40.000 0.00 0.00 37.69 3.27
3593 3892 8.843308 AAATCAATCTCTCCCCAATTTCATTA 57.157 30.769 0.00 0.00 0.00 1.90
3627 3926 4.439305 TGTGCAAGCCAATCTAATCAAC 57.561 40.909 0.00 0.00 0.00 3.18
3725 4024 5.695851 AATTCTGACTTGTAAACAGCAGG 57.304 39.130 0.00 0.00 0.00 4.85
3729 4028 9.139174 ACAAACAAAATTCTGACTTGTAAACAG 57.861 29.630 3.27 0.00 33.05 3.16
3772 4071 7.253950 GCTTTTGCAAATAAGTTTTCTTCACGA 60.254 33.333 13.65 0.00 46.58 4.35
4000 4299 7.402071 TCTCCTGGTAACCAATAGTTCACTTAT 59.598 37.037 0.00 0.00 40.05 1.73
4094 4393 8.535335 AGTGAAGTCATAGACTCACAACAATAT 58.465 33.333 20.81 6.28 42.59 1.28
4099 4398 6.451393 AGAAGTGAAGTCATAGACTCACAAC 58.549 40.000 20.81 16.21 42.59 3.32
4121 4420 6.874664 GTCATATATAGGACAGACAGACGAGA 59.125 42.308 19.89 0.00 37.01 4.04
4218 4517 8.393671 ACTTGTTACGGGATGTTTATTTTACA 57.606 30.769 0.00 0.00 0.00 2.41
4322 4621 5.925506 TGGTACAACAAGCTACAGCTATA 57.074 39.130 3.74 0.00 44.57 1.31
4343 4642 5.067674 TCCTAGGCAATTTTCGGAATGATTG 59.932 40.000 2.96 16.68 33.71 2.67


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

AutoCloner maintained by Alex Coulton.