Multiple sequence alignment - TraesCS6B01G120100

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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 TraesCS6B01G120100 chr6B 100.000 2449 0 0 1 2449 114882818 114885266 0.000000e+00 4523.0
1 TraesCS6B01G120100 chr6B 94.670 788 16 5 378 1147 115063357 115064136 0.000000e+00 1199.0
2 TraesCS6B01G120100 chr6B 96.639 595 14 2 988 1576 115038900 115039494 0.000000e+00 983.0
3 TraesCS6B01G120100 chr6B 84.701 536 46 14 699 1225 115537072 115537580 1.010000e-138 503.0
4 TraesCS6B01G120100 chr6B 78.935 845 86 42 771 1574 115068216 115069009 7.870000e-135 490.0
5 TraesCS6B01G120100 chr6B 85.285 333 30 6 1 319 115037422 115037749 2.350000e-85 326.0
6 TraesCS6B01G120100 chr6B 86.395 294 28 8 487 770 115038039 115038330 6.580000e-81 311.0
7 TraesCS6B01G120100 chr6B 89.773 176 10 3 316 490 115037779 115037947 4.100000e-53 219.0
8 TraesCS6B01G120100 chr6B 98.551 69 1 0 1506 1574 115064139 115064207 3.310000e-24 122.0
9 TraesCS6B01G120100 chr6B 90.541 74 3 3 1333 1402 115537708 115537781 7.210000e-16 95.3
10 TraesCS6B01G120100 chr6B 98.000 50 1 0 780 829 115068165 115068214 1.210000e-13 87.9
11 TraesCS6B01G120100 chr7B 94.857 875 42 3 1577 2449 142414886 142415759 0.000000e+00 1363.0
12 TraesCS6B01G120100 chr7B 94.533 878 42 6 1575 2449 560801618 560800744 0.000000e+00 1351.0
13 TraesCS6B01G120100 chr7B 94.231 884 46 5 1569 2449 720529077 720528196 0.000000e+00 1345.0
14 TraesCS6B01G120100 chr2B 94.677 883 39 7 1571 2449 87799368 87798490 0.000000e+00 1363.0
15 TraesCS6B01G120100 chr2B 93.545 883 54 3 1569 2449 43428357 43429238 0.000000e+00 1312.0
16 TraesCS6B01G120100 chr4B 95.035 866 42 1 1585 2449 27767204 27768069 0.000000e+00 1360.0
17 TraesCS6B01G120100 chr4B 94.653 879 41 3 1572 2449 139064454 139065327 0.000000e+00 1358.0
18 TraesCS6B01G120100 chr4B 93.950 876 48 5 1577 2449 95349473 95350346 0.000000e+00 1319.0
19 TraesCS6B01G120100 chr5B 94.413 877 43 6 1576 2449 541970690 541969817 0.000000e+00 1343.0
20 TraesCS6B01G120100 chr6D 81.343 804 99 28 742 1524 46840528 46841301 7.490000e-170 606.0
21 TraesCS6B01G120100 chr6D 89.597 471 20 15 497 948 46445993 46446453 2.730000e-159 571.0
22 TraesCS6B01G120100 chr6D 83.385 644 69 18 941 1556 46453601 46454234 1.640000e-156 562.0
23 TraesCS6B01G120100 chr6D 76.961 816 102 38 739 1498 46842780 46843565 1.060000e-103 387.0
24 TraesCS6B01G120100 chr6D 86.713 286 29 6 852 1133 46811079 46811359 2.370000e-80 309.0
25 TraesCS6B01G120100 chr6D 74.675 462 73 19 1091 1524 46067007 46067452 5.420000e-37 165.0
26 TraesCS6B01G120100 chr6D 81.890 127 16 2 1254 1374 46811477 46811602 1.550000e-17 100.0
27 TraesCS6B01G120100 chr6A 77.273 858 113 47 738 1543 60389703 60390530 1.740000e-116 429.0


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 TraesCS6B01G120100 chr6B 114882818 114885266 2448 False 4523.000 4523 100.0000 1 2449 1 chr6B.!!$F1 2448
1 TraesCS6B01G120100 chr6B 115063357 115069009 5652 False 474.725 1199 92.5390 378 1574 4 chr6B.!!$F3 1196
2 TraesCS6B01G120100 chr6B 115037422 115039494 2072 False 459.750 983 89.5230 1 1576 4 chr6B.!!$F2 1575
3 TraesCS6B01G120100 chr6B 115537072 115537781 709 False 299.150 503 87.6210 699 1402 2 chr6B.!!$F4 703
4 TraesCS6B01G120100 chr7B 142414886 142415759 873 False 1363.000 1363 94.8570 1577 2449 1 chr7B.!!$F1 872
5 TraesCS6B01G120100 chr7B 560800744 560801618 874 True 1351.000 1351 94.5330 1575 2449 1 chr7B.!!$R1 874
6 TraesCS6B01G120100 chr7B 720528196 720529077 881 True 1345.000 1345 94.2310 1569 2449 1 chr7B.!!$R2 880
7 TraesCS6B01G120100 chr2B 87798490 87799368 878 True 1363.000 1363 94.6770 1571 2449 1 chr2B.!!$R1 878
8 TraesCS6B01G120100 chr2B 43428357 43429238 881 False 1312.000 1312 93.5450 1569 2449 1 chr2B.!!$F1 880
9 TraesCS6B01G120100 chr4B 27767204 27768069 865 False 1360.000 1360 95.0350 1585 2449 1 chr4B.!!$F1 864
10 TraesCS6B01G120100 chr4B 139064454 139065327 873 False 1358.000 1358 94.6530 1572 2449 1 chr4B.!!$F3 877
11 TraesCS6B01G120100 chr4B 95349473 95350346 873 False 1319.000 1319 93.9500 1577 2449 1 chr4B.!!$F2 872
12 TraesCS6B01G120100 chr5B 541969817 541970690 873 True 1343.000 1343 94.4130 1576 2449 1 chr5B.!!$R1 873
13 TraesCS6B01G120100 chr6D 46453601 46454234 633 False 562.000 562 83.3850 941 1556 1 chr6D.!!$F3 615
14 TraesCS6B01G120100 chr6D 46840528 46843565 3037 False 496.500 606 79.1520 739 1524 2 chr6D.!!$F5 785
15 TraesCS6B01G120100 chr6D 46811079 46811602 523 False 204.500 309 84.3015 852 1374 2 chr6D.!!$F4 522
16 TraesCS6B01G120100 chr6A 60389703 60390530 827 False 429.000 429 77.2730 738 1543 1 chr6A.!!$F1 805

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
331 378 1.138859 TGGATACCTGCAGAATCCACG 59.861 52.381 31.29 12.82 43.27 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2290 9694 0.248289 AAGGATGGCAAGCAACATGC 59.752 50.0 0.0 0.0 45.46 4.06 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
46 47 5.242393 AGAACATCAACACCCATTTCAAGAG 59.758 40.000 0.00 0.00 0.00 2.85
55 56 3.456277 ACCCATTTCAAGAGCCCTAGTAG 59.544 47.826 0.00 0.00 0.00 2.57
69 70 7.036498 AGAGCCCTAGTAGTAATATCCTCATCA 60.036 40.741 0.00 0.00 0.00 3.07
73 74 9.130661 CCCTAGTAGTAATATCCTCATCATCTG 57.869 40.741 0.00 0.00 0.00 2.90
101 102 5.983540 AGTAAAAGCATTCTGAGAGGTAGG 58.016 41.667 0.00 0.00 0.00 3.18
105 106 2.246067 AGCATTCTGAGAGGTAGGAGGA 59.754 50.000 0.00 0.00 0.00 3.71
111 112 5.055265 TCTGAGAGGTAGGAGGAGTTATG 57.945 47.826 0.00 0.00 0.00 1.90
113 114 2.894765 GAGAGGTAGGAGGAGTTATGCC 59.105 54.545 0.00 0.00 0.00 4.40
115 116 3.051727 AGAGGTAGGAGGAGTTATGCCTT 60.052 47.826 0.00 0.00 35.44 4.35
123 124 4.080526 GGAGGAGTTATGCCTTCCAAGTTA 60.081 45.833 0.00 0.00 35.44 2.24
129 130 7.773690 GGAGTTATGCCTTCCAAGTTATTCTTA 59.226 37.037 0.00 0.00 34.66 2.10
130 131 8.738645 AGTTATGCCTTCCAAGTTATTCTTAG 57.261 34.615 0.00 0.00 34.66 2.18
131 132 7.283354 AGTTATGCCTTCCAAGTTATTCTTAGC 59.717 37.037 0.00 0.00 34.66 3.09
132 133 4.917385 TGCCTTCCAAGTTATTCTTAGCA 58.083 39.130 0.00 0.00 34.66 3.49
133 134 4.943705 TGCCTTCCAAGTTATTCTTAGCAG 59.056 41.667 0.00 0.00 34.66 4.24
152 153 1.277557 AGCAACCTCAGAGATGGTGAC 59.722 52.381 0.00 0.00 36.57 3.67
182 184 3.965347 GGTCTGTTATTCCCCTAGTAGCA 59.035 47.826 0.00 0.00 0.00 3.49
188 190 7.512746 TCTGTTATTCCCCTAGTAGCATGTATT 59.487 37.037 0.00 0.00 0.00 1.89
226 228 6.859112 AATCGGAGGATTAGCAGTATACAT 57.141 37.500 5.50 0.00 41.05 2.29
227 229 6.859112 ATCGGAGGATTAGCAGTATACATT 57.141 37.500 5.50 0.00 0.00 2.71
232 243 7.542477 CGGAGGATTAGCAGTATACATTAACAG 59.458 40.741 5.50 0.00 0.00 3.16
240 251 5.991606 GCAGTATACATTAACAGATCCAGCA 59.008 40.000 5.50 0.00 0.00 4.41
262 273 3.593942 TCCTGGGAAGGTTGAGTAAGAA 58.406 45.455 0.00 0.00 0.00 2.52
270 281 4.545208 AGGTTGAGTAAGAAGAGCTTCC 57.455 45.455 6.61 0.00 40.33 3.46
281 292 2.244486 AGAGCTTCCTCATCCACAGA 57.756 50.000 0.00 0.00 40.68 3.41
310 325 6.716284 TCCACAACATCTTACATCCACAATA 58.284 36.000 0.00 0.00 0.00 1.90
331 378 1.138859 TGGATACCTGCAGAATCCACG 59.861 52.381 31.29 12.82 43.27 4.94
352 400 2.224548 GGTACCAGAACAACAGAGCCTT 60.225 50.000 7.15 0.00 0.00 4.35
361 409 2.174854 ACAACAGAGCCTTAAACCTGGT 59.825 45.455 0.00 0.00 0.00 4.00
366 414 2.569404 AGAGCCTTAAACCTGGTGAGAG 59.431 50.000 0.00 0.00 0.00 3.20
375 423 4.373156 AACCTGGTGAGAGCTGTTATTT 57.627 40.909 0.00 0.00 0.00 1.40
405 453 9.445878 GATTCATCCACATATCACACTTATCAT 57.554 33.333 0.00 0.00 0.00 2.45
612 755 7.441157 CAGTCTTTTACATGGTTTCACTACTGA 59.559 37.037 0.00 0.00 31.97 3.41
620 783 7.450074 ACATGGTTTCACTACTGAAATGTCTA 58.550 34.615 0.00 0.00 45.93 2.59
697 861 7.122799 ACACTACTTACTCATCTCTGTATGCAA 59.877 37.037 0.00 0.00 0.00 4.08
1479 8871 3.512516 GGTGCGGCATGGAAGCTC 61.513 66.667 5.72 0.00 34.17 4.09
1545 8940 3.370978 GGTTATGACAGACGGTTGATGTG 59.629 47.826 0.20 0.00 0.00 3.21
1962 9363 1.403814 CCAGCCCTTCAGAGACGATA 58.596 55.000 0.00 0.00 0.00 2.92
1987 9388 6.488715 AGCTAAAATCAGGTGAAAATCTCCT 58.511 36.000 0.00 0.00 40.71 3.69
2227 9630 6.774673 TGAAATAAAGGGGGTTGGAAAAATC 58.225 36.000 0.00 0.00 0.00 2.17
2229 9632 6.373005 AATAAAGGGGGTTGGAAAAATCAG 57.627 37.500 0.00 0.00 0.00 2.90
2290 9694 0.905357 AGTAGCTGCCACCTAGTTGG 59.095 55.000 1.03 1.03 42.93 3.77
2308 9712 1.895238 GCATGTTGCTTGCCATCCT 59.105 52.632 0.00 0.00 40.96 3.24
2362 9766 6.289834 ACAATTCTTGTGGATTTTTGATGCA 58.710 32.000 0.00 0.00 43.48 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 7.782644 AGATGATGAGGATATTACTACTAGGGC 59.217 40.741 0.00 0.00 0.00 5.19
75 76 8.861086 CCTACCTCTCAGAATGCTTTTACTATA 58.139 37.037 0.00 0.00 34.76 1.31
77 78 6.895756 TCCTACCTCTCAGAATGCTTTTACTA 59.104 38.462 0.00 0.00 34.76 1.82
80 81 5.129485 CCTCCTACCTCTCAGAATGCTTTTA 59.871 44.000 0.00 0.00 34.76 1.52
90 91 3.572255 GCATAACTCCTCCTACCTCTCAG 59.428 52.174 0.00 0.00 0.00 3.35
101 102 3.636153 ACTTGGAAGGCATAACTCCTC 57.364 47.619 0.00 0.00 32.45 3.71
105 106 7.283354 GCTAAGAATAACTTGGAAGGCATAACT 59.717 37.037 0.00 0.00 39.02 2.24
111 112 4.201960 GCTGCTAAGAATAACTTGGAAGGC 60.202 45.833 0.00 0.00 41.34 4.35
113 114 6.317857 GTTGCTGCTAAGAATAACTTGGAAG 58.682 40.000 0.00 0.00 43.13 3.46
115 116 4.700213 GGTTGCTGCTAAGAATAACTTGGA 59.300 41.667 0.00 0.00 39.02 3.53
123 124 3.517100 TCTCTGAGGTTGCTGCTAAGAAT 59.483 43.478 4.59 0.00 0.00 2.40
129 130 0.252479 CCATCTCTGAGGTTGCTGCT 59.748 55.000 4.59 0.00 0.00 4.24
130 131 0.035630 ACCATCTCTGAGGTTGCTGC 60.036 55.000 4.59 0.00 33.39 5.25
131 132 1.277273 TCACCATCTCTGAGGTTGCTG 59.723 52.381 4.59 1.91 35.52 4.41
132 133 1.277557 GTCACCATCTCTGAGGTTGCT 59.722 52.381 4.59 0.00 35.52 3.91
133 134 1.002430 TGTCACCATCTCTGAGGTTGC 59.998 52.381 4.59 0.00 35.52 4.17
152 153 2.159085 GGGAATAACAGACCCGTCTCTG 60.159 54.545 5.29 5.29 43.06 3.35
154 155 1.138464 GGGGAATAACAGACCCGTCTC 59.862 57.143 0.00 0.00 44.09 3.36
168 169 5.846714 ACAGAATACATGCTACTAGGGGAAT 59.153 40.000 0.00 0.00 0.00 3.01
219 221 7.332926 CAGGATGCTGGATCTGTTAATGTATAC 59.667 40.741 6.28 0.00 0.00 1.47
222 224 5.614308 CAGGATGCTGGATCTGTTAATGTA 58.386 41.667 6.28 0.00 0.00 2.29
223 225 4.458397 CAGGATGCTGGATCTGTTAATGT 58.542 43.478 6.28 0.00 0.00 2.71
240 251 3.803340 TCTTACTCAACCTTCCCAGGAT 58.197 45.455 0.00 0.00 44.19 3.24
262 273 2.244486 TCTGTGGATGAGGAAGCTCT 57.756 50.000 0.00 0.00 0.00 4.09
281 292 6.009589 TGGATGTAAGATGTTGTGGAAACAT 58.990 36.000 3.47 3.47 46.14 2.71
287 298 5.902613 ATTGTGGATGTAAGATGTTGTGG 57.097 39.130 0.00 0.00 0.00 4.17
310 325 2.224378 CGTGGATTCTGCAGGTATCCAT 60.224 50.000 34.24 13.84 46.81 3.41
313 328 1.139058 ACCGTGGATTCTGCAGGTATC 59.861 52.381 15.13 16.14 0.00 2.24
319 334 0.249120 CTGGTACCGTGGATTCTGCA 59.751 55.000 7.57 0.00 0.00 4.41
321 336 2.028476 TGTTCTGGTACCGTGGATTCTG 60.028 50.000 7.57 0.00 0.00 3.02
331 378 1.348036 AGGCTCTGTTGTTCTGGTACC 59.652 52.381 4.43 4.43 0.00 3.34
352 400 5.499004 AATAACAGCTCTCACCAGGTTTA 57.501 39.130 0.00 0.00 0.00 2.01
361 409 6.053632 TGAATCTCCAAATAACAGCTCTCA 57.946 37.500 0.00 0.00 0.00 3.27
366 414 5.357878 TGTGGATGAATCTCCAAATAACAGC 59.642 40.000 3.60 0.00 46.66 4.40
375 423 5.367644 AGTGTGATATGTGGATGAATCTCCA 59.632 40.000 0.00 0.00 43.09 3.86
405 453 1.476833 GCAACTGTTGGAGACCAGGAA 60.477 52.381 21.01 0.00 33.81 3.36
648 812 5.183331 GTCCATAACTTCCCCTGTTTTCTTC 59.817 44.000 0.00 0.00 0.00 2.87
655 819 2.632537 AGTGTCCATAACTTCCCCTGT 58.367 47.619 0.00 0.00 0.00 4.00
939 1544 4.980805 TCGTTGGGCTGCACGGTC 62.981 66.667 10.47 0.00 37.02 4.79
1478 8870 2.854736 TCATCATCAGTCCCAGGAGA 57.145 50.000 0.00 0.00 0.00 3.71
1479 8871 2.970640 TGATCATCATCAGTCCCAGGAG 59.029 50.000 0.00 0.00 33.80 3.69
1962 9363 6.950619 AGGAGATTTTCACCTGATTTTAGCTT 59.049 34.615 0.00 0.00 36.09 3.74
1987 9388 6.269538 CCTGAAGGATGAGAAGGATGAGATAA 59.730 42.308 0.00 0.00 37.39 1.75
2227 9630 2.538737 CGTTGTACACAAGTGGCAACTG 60.539 50.000 25.26 19.23 42.57 3.16
2229 9632 1.666700 TCGTTGTACACAAGTGGCAAC 59.333 47.619 21.72 21.72 41.99 4.17
2290 9694 0.248289 AAGGATGGCAAGCAACATGC 59.752 50.000 0.00 0.00 45.46 4.06
2308 9712 7.112452 TCTACTGCTTGCACATAGAAGATAA 57.888 36.000 0.00 0.00 0.00 1.75
2362 9766 5.691896 TCTCAATCCTGCATGATCAAGAAT 58.308 37.500 4.86 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.