Multiple sequence alignment - TraesCS5B01G555600

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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 TraesCS5B01G555600 chr5B 100.000 3497 0 0 1 3497 704761685 704758189 0.000000e+00 6458
1 TraesCS5B01G555600 chr5B 90.842 1758 108 25 1079 2798 704498339 704500081 0.000000e+00 2305
2 TraesCS5B01G555600 chr5B 87.576 1489 158 15 1052 2526 704824488 704823013 0.000000e+00 1700
3 TraesCS5B01G555600 chr5B 87.383 1490 160 16 1052 2526 704479165 704480641 0.000000e+00 1685
4 TraesCS5B01G555600 chr5B 84.688 1489 198 21 1060 2528 704723269 704724747 0.000000e+00 1459
5 TraesCS5B01G555600 chr5B 82.056 1488 228 26 1052 2520 704528544 704530011 0.000000e+00 1232
6 TraesCS5B01G555600 chr5B 84.645 788 103 13 1765 2539 704320970 704320188 0.000000e+00 769
7 TraesCS5B01G555600 chr5B 92.615 501 31 6 2794 3290 704500124 704500622 0.000000e+00 715
8 TraesCS5B01G555600 chr5B 82.085 614 82 19 2868 3480 704318364 704317778 1.870000e-137 499
9 TraesCS5B01G555600 chr5B 92.550 349 20 2 194 537 704497391 704497738 2.420000e-136 496
10 TraesCS5B01G555600 chr5B 96.744 215 7 0 3283 3497 704500962 704501176 3.320000e-95 359
11 TraesCS5B01G555600 chr5B 86.275 255 9 5 709 963 704497828 704498056 1.610000e-63 254
12 TraesCS5B01G555600 chr4A 95.187 2805 54 37 1 2795 610705839 610708572 0.000000e+00 4357
13 TraesCS5B01G555600 chr4A 92.378 1758 91 22 1079 2798 611073503 611071751 0.000000e+00 2464
14 TraesCS5B01G555600 chr4A 87.047 1490 165 16 1052 2526 611203507 611202031 0.000000e+00 1657
15 TraesCS5B01G555600 chr4A 86.568 1489 174 13 1052 2526 610640280 610641756 0.000000e+00 1618
16 TraesCS5B01G555600 chr4A 84.869 1487 199 18 1060 2528 611025663 611027141 0.000000e+00 1476
17 TraesCS5B01G555600 chr4A 82.701 1503 226 25 1052 2539 610818295 610816812 0.000000e+00 1304
18 TraesCS5B01G555600 chr4A 93.028 502 28 7 2794 3290 611071708 611071209 0.000000e+00 726
19 TraesCS5B01G555600 chr4A 93.000 500 29 6 2794 3290 610708618 610709114 0.000000e+00 725
20 TraesCS5B01G555600 chr4A 92.654 422 26 3 1 422 611080161 611079745 1.390000e-168 603
21 TraesCS5B01G555600 chr4A 85.714 224 6 4 3274 3497 610709446 610709643 2.730000e-51 213
22 TraesCS5B01G555600 chr4A 83.486 218 7 2 746 963 611073998 611073810 3.590000e-40 176
23 TraesCS5B01G555600 chr4A 83.410 217 6 8 3283 3497 611070868 611070680 1.290000e-39 174


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 TraesCS5B01G555600 chr5B 704758189 704761685 3496 True 6458.0 6458 100.000000 1 3497 1 chr5B.!!$R1 3496
1 TraesCS5B01G555600 chr5B 704823013 704824488 1475 True 1700.0 1700 87.576000 1052 2526 1 chr5B.!!$R2 1474
2 TraesCS5B01G555600 chr5B 704479165 704480641 1476 False 1685.0 1685 87.383000 1052 2526 1 chr5B.!!$F1 1474
3 TraesCS5B01G555600 chr5B 704723269 704724747 1478 False 1459.0 1459 84.688000 1060 2528 1 chr5B.!!$F3 1468
4 TraesCS5B01G555600 chr5B 704528544 704530011 1467 False 1232.0 1232 82.056000 1052 2520 1 chr5B.!!$F2 1468
5 TraesCS5B01G555600 chr5B 704497391 704501176 3785 False 825.8 2305 91.805200 194 3497 5 chr5B.!!$F4 3303
6 TraesCS5B01G555600 chr5B 704317778 704320970 3192 True 634.0 769 83.365000 1765 3480 2 chr5B.!!$R3 1715
7 TraesCS5B01G555600 chr4A 610705839 610709643 3804 False 1765.0 4357 91.300333 1 3497 3 chr4A.!!$F3 3496
8 TraesCS5B01G555600 chr4A 611202031 611203507 1476 True 1657.0 1657 87.047000 1052 2526 1 chr4A.!!$R3 1474
9 TraesCS5B01G555600 chr4A 610640280 610641756 1476 False 1618.0 1618 86.568000 1052 2526 1 chr4A.!!$F1 1474
10 TraesCS5B01G555600 chr4A 611025663 611027141 1478 False 1476.0 1476 84.869000 1060 2528 1 chr4A.!!$F2 1468
11 TraesCS5B01G555600 chr4A 610816812 610818295 1483 True 1304.0 1304 82.701000 1052 2539 1 chr4A.!!$R1 1487
12 TraesCS5B01G555600 chr4A 611070680 611073998 3318 True 885.0 2464 88.075500 746 3497 4 chr4A.!!$R4 2751

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
376 382 0.446222 ATCAAATCAAACGGACGCGG 59.554 50.000 12.47 0.0 0.0 6.46 F
423 429 1.724623 GTGAACGCTCGTCAATTAGCA 59.275 47.619 0.00 0.0 38.7 3.49 F
1647 1909 3.007074 TGGAACAGTATCGTGGCAAGTTA 59.993 43.478 0.00 0.0 0.0 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1647 1909 2.574006 TGATTGCAAGCTCTTCCACT 57.426 45.000 16.73 0.00 0.00 4.00 R
1734 1996 7.096065 GCTAAATCAAAAACTAGTGCCTTTGTG 60.096 37.037 17.96 6.93 32.00 3.33 R
3358 5541 1.203050 AGGAGCTAGCAGAGGAGATCC 60.203 57.143 18.83 12.20 46.58 3.36 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
376 382 0.446222 ATCAAATCAAACGGACGCGG 59.554 50.000 12.47 0.00 0.00 6.46
391 397 2.441532 CGGGGGAGTTCGCTAGGA 60.442 66.667 0.00 0.00 0.00 2.94
423 429 1.724623 GTGAACGCTCGTCAATTAGCA 59.275 47.619 0.00 0.00 38.70 3.49
532 538 7.981225 CCACACCAATAATAAGCTGCTAAAAAT 59.019 33.333 0.90 0.00 0.00 1.82
575 581 3.125573 GTTTTCCTCTCCGCCGGC 61.126 66.667 19.07 19.07 0.00 6.13
576 582 4.404098 TTTTCCTCTCCGCCGGCC 62.404 66.667 23.46 2.84 0.00 6.13
583 589 4.840005 CTCCGCCGGCCTTCCTTC 62.840 72.222 23.46 0.00 0.00 3.46
1123 1341 6.376864 AGCTATATCAGAGCACATAAGACGAT 59.623 38.462 0.00 0.00 42.69 3.73
1216 1434 3.686227 TCCATGCCAAGGGAATAACAT 57.314 42.857 0.00 0.00 31.97 2.71
1647 1909 3.007074 TGGAACAGTATCGTGGCAAGTTA 59.993 43.478 0.00 0.00 0.00 2.24
1734 1996 1.456732 GTTTTGCTGTATCATCGCGC 58.543 50.000 0.00 0.00 0.00 6.86
1797 2059 1.482182 CCTCCAGGTTGTCATGATCGA 59.518 52.381 0.00 0.00 0.00 3.59
2494 2770 2.235898 GTGAGGTCTGCTCCTTTCATCT 59.764 50.000 0.00 0.00 38.02 2.90
2663 4420 8.405531 GCTGGACAGTTTCTTTTATTGCATATA 58.594 33.333 0.82 0.00 0.00 0.86
2752 4509 7.280356 TCTCTTTGTTTGGAAGCTACTAGTTT 58.720 34.615 0.00 0.00 0.00 2.66
2837 4663 5.936686 ATCCTTCGCATCATACTTCATTG 57.063 39.130 0.00 0.00 0.00 2.82
2890 4718 6.147985 TGGTTTTTGGTTTAAACTTGCAGTTC 59.852 34.615 17.50 0.00 37.47 3.01
2899 4727 0.822121 ACTTGCAGTTCCGTTTCCCC 60.822 55.000 0.00 0.00 0.00 4.81
2926 4754 2.030457 CGTGCATTCGGTACAAGAATCC 59.970 50.000 11.41 5.40 31.67 3.01
2983 4811 9.274065 CTGTTCAACAACTTAAAGAGTTTGTAC 57.726 33.333 0.00 0.00 46.34 2.90
2984 4812 8.784994 TGTTCAACAACTTAAAGAGTTTGTACA 58.215 29.630 0.00 0.00 46.34 2.90
3073 4901 7.439655 CCTGCACTGGAGATTTTAAGTATAGAC 59.560 40.741 0.00 0.00 0.00 2.59
3107 4935 1.213296 TCCCCTAGAAGGCCATGAAC 58.787 55.000 5.01 0.00 32.73 3.18
3120 4948 2.228822 GCCATGAACAGGACACGAAAAT 59.771 45.455 0.00 0.00 0.00 1.82
3132 4960 1.778591 CACGAAAATGGTTGTTGACGC 59.221 47.619 0.00 0.00 0.00 5.19
3199 5027 5.680619 TCCAAGTGCACCCTAATATTACTG 58.319 41.667 14.63 0.00 0.00 2.74
3209 5037 7.390718 GCACCCTAATATTACTGTAAGGGATTG 59.609 40.741 22.45 14.48 45.53 2.67
3220 5048 5.968167 ACTGTAAGGGATTGGTTGGTATAGA 59.032 40.000 0.00 0.00 39.30 1.98
3258 5086 1.312884 AGCTGGGGATGGAAAATCCT 58.687 50.000 4.46 0.00 37.46 3.24
3261 5089 3.468625 AGCTGGGGATGGAAAATCCTATT 59.531 43.478 4.46 0.00 37.46 1.73
3264 5093 2.899900 GGGGATGGAAAATCCTATTGGC 59.100 50.000 4.46 0.00 37.46 4.52
3280 5109 3.951775 TTGGCGGCATCTTTAAACATT 57.048 38.095 14.32 0.00 0.00 2.71
3281 5110 3.229276 TGGCGGCATCTTTAAACATTG 57.771 42.857 7.97 0.00 0.00 2.82
3358 5541 0.688487 TTCCTCTGGTTACCGGTTGG 59.312 55.000 15.04 13.20 42.84 3.77
3360 5543 1.196104 CCTCTGGTTACCGGTTGGGA 61.196 60.000 15.04 3.81 40.75 4.37
3392 5575 4.648626 TCCTGCTGGCCTGTGCAC 62.649 66.667 10.75 10.75 40.13 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
376 382 0.460722 GAACTCCTAGCGAACTCCCC 59.539 60.000 0.00 0.00 0.00 4.81
391 397 1.689273 AGCGTTCACTGAGAAGGAACT 59.311 47.619 10.89 0.00 43.12 3.01
423 429 4.974399 CCTTTTCGGGAGCTTCCTATAAT 58.026 43.478 10.06 0.00 36.57 1.28
585 591 3.902086 GAGTACGGCGAGGGCTCC 61.902 72.222 16.62 0.00 39.81 4.70
586 592 2.829458 AGAGTACGGCGAGGGCTC 60.829 66.667 16.62 14.46 39.81 4.70
645 663 4.410400 GAGGAGGCGTTGGGGTGG 62.410 72.222 0.00 0.00 0.00 4.61
1123 1341 5.525745 TCAGCTTTCGATCAAACACTTTACA 59.474 36.000 0.00 0.00 0.00 2.41
1216 1434 4.503910 CACAGTTTACATCGATCTTCCCA 58.496 43.478 0.00 0.00 0.00 4.37
1647 1909 2.574006 TGATTGCAAGCTCTTCCACT 57.426 45.000 16.73 0.00 0.00 4.00
1734 1996 7.096065 GCTAAATCAAAAACTAGTGCCTTTGTG 60.096 37.037 17.96 6.93 32.00 3.33
1789 2051 9.177304 CTCAAATGGAAATTTGTATCGATCATG 57.823 33.333 0.00 0.00 41.10 3.07
2494 2770 5.251764 ACTTACGTCCAGCTCTAACTTCTA 58.748 41.667 0.00 0.00 0.00 2.10
2663 4420 2.242965 TCCATCAATTCCAGGACAGCAT 59.757 45.455 0.00 0.00 0.00 3.79
2664 4421 1.634973 TCCATCAATTCCAGGACAGCA 59.365 47.619 0.00 0.00 0.00 4.41
2677 4434 7.797121 TTAGCAGTCTATATCCATCCATCAA 57.203 36.000 0.00 0.00 0.00 2.57
2776 4534 9.831737 CGAAAGTCAAATTGTCATCTTATTTCT 57.168 29.630 0.00 0.00 0.00 2.52
2784 4542 8.665685 ACTATTACCGAAAGTCAAATTGTCATC 58.334 33.333 0.00 0.00 0.00 2.92
2890 4718 1.571215 GCACGTAACTGGGGAAACGG 61.571 60.000 0.00 0.00 39.57 4.44
2899 4727 2.330286 TGTACCGAATGCACGTAACTG 58.670 47.619 0.00 0.00 0.00 3.16
2926 4754 3.742433 AGCTTCCTGATAGGTTCATCG 57.258 47.619 0.00 0.00 36.53 3.84
2983 4811 6.361481 CGATGCATGCTTTAAATCCTGTAATG 59.639 38.462 20.33 0.00 0.00 1.90
2984 4812 6.441274 CGATGCATGCTTTAAATCCTGTAAT 58.559 36.000 20.33 0.00 0.00 1.89
3073 4901 6.439636 TCTAGGGGATATTTGTCTGAATGG 57.560 41.667 0.00 0.00 0.00 3.16
3107 4935 3.066064 TCAACAACCATTTTCGTGTCCTG 59.934 43.478 0.00 0.00 0.00 3.86
3120 4948 2.589442 GGACCGCGTCAACAACCA 60.589 61.111 4.92 0.00 33.68 3.67
3132 4960 4.202264 ACCTTCTAGCAATTCTATGGACCG 60.202 45.833 0.00 0.00 0.00 4.79
3199 5027 6.742559 TCTCTATACCAACCAATCCCTTAC 57.257 41.667 0.00 0.00 0.00 2.34
3209 5037 9.640963 GATACAATGTACATCTCTATACCAACC 57.359 37.037 9.23 0.00 0.00 3.77
3220 5048 6.210385 CCCAGCTAGAGATACAATGTACATCT 59.790 42.308 9.23 12.12 0.00 2.90
3240 5068 3.532641 ATAGGATTTTCCATCCCCAGC 57.467 47.619 0.00 0.00 39.61 4.85
3243 5071 2.899900 GCCAATAGGATTTTCCATCCCC 59.100 50.000 0.00 0.00 39.61 4.81
3258 5086 5.126222 TCAATGTTTAAAGATGCCGCCAATA 59.874 36.000 0.00 0.00 0.00 1.90
3261 5089 2.822561 TCAATGTTTAAAGATGCCGCCA 59.177 40.909 0.00 0.00 0.00 5.69
3264 5093 3.853671 GCAGTCAATGTTTAAAGATGCCG 59.146 43.478 0.00 0.00 0.00 5.69
3280 5109 6.409704 AGAATTATACAGAAGCAAGCAGTCA 58.590 36.000 0.00 0.00 0.00 3.41
3281 5110 6.917217 AGAATTATACAGAAGCAAGCAGTC 57.083 37.500 0.00 0.00 0.00 3.51
3358 5541 1.203050 AGGAGCTAGCAGAGGAGATCC 60.203 57.143 18.83 12.20 46.58 3.36
3360 5543 1.999648 CAGGAGCTAGCAGAGGAGAT 58.000 55.000 18.83 0.00 0.00 2.75


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

AutoCloner maintained by Alex Coulton.