Multiple sequence alignment - TraesCS7D01G032300

Loading Multiple Alignment...

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 TraesCS7D01G032300 chr7D 100.000 5110 0 0 1 5110 16762728 16757619 0.000000e+00 9437
1 TraesCS7D01G032300 chr7D 95.570 4853 202 12 1 4841 17119884 17124735 0.000000e+00 7758
2 TraesCS7D01G032300 chr7D 95.250 2505 112 7 1 2500 16993323 16995825 0.000000e+00 3960
3 TraesCS7D01G032300 chr7D 100.000 335 0 0 4407 4741 16995822 16996156 2.020000e-173 619
4 TraesCS7D01G032300 chr7D 95.882 340 13 1 4771 5110 16996151 16996489 2.690000e-152 549
5 TraesCS7D01G032300 chr7D 93.644 236 14 1 4875 5110 17124730 17124964 8.140000e-93 351
6 TraesCS7D01G032300 chr4A 95.281 5128 188 20 1 5110 717262521 717257430 0.000000e+00 8080
7 TraesCS7D01G032300 chr4A 95.351 4474 181 13 1 4464 717750998 717755454 0.000000e+00 7084
8 TraesCS7D01G032300 chr4A 95.504 3492 136 11 1234 4718 717803039 717806516 0.000000e+00 5559
9 TraesCS7D01G032300 chr4A 95.050 3030 127 13 1207 4230 717287668 717284656 0.000000e+00 4743
10 TraesCS7D01G032300 chr4A 95.882 2477 96 6 1757 4230 717225661 717223188 0.000000e+00 4004
11 TraesCS7D01G032300 chr4A 95.230 1237 54 3 1 1235 717801702 717802935 0.000000e+00 1953
12 TraesCS7D01G032300 chr4A 94.602 778 40 2 1 776 717235527 717234750 0.000000e+00 1203
13 TraesCS7D01G032300 chr4A 94.343 654 24 3 4216 4866 717223176 717222533 0.000000e+00 990
14 TraesCS7D01G032300 chr4A 96.264 455 15 2 4216 4668 717284644 717284190 0.000000e+00 745
15 TraesCS7D01G032300 chr4A 95.726 351 13 2 4760 5110 717806523 717806871 9.600000e-157 564
16 TraesCS7D01G032300 chr4A 94.444 288 12 3 4582 4866 717755454 717755740 1.690000e-119 440
17 TraesCS7D01G032300 chr4A 93.657 268 8 3 4851 5110 717222519 717222253 4.800000e-105 392
18 TraesCS7D01G032300 chr4A 92.537 268 11 3 4851 5110 717755753 717756019 4.830000e-100 375
19 TraesCS7D01G032300 chr7A 94.090 5127 239 32 1 5110 16424946 16430025 0.000000e+00 7731
20 TraesCS7D01G032300 chr7A 94.770 4245 197 12 1 4239 16312851 16317076 0.000000e+00 6586
21 TraesCS7D01G032300 chr7A 93.847 2779 135 14 2 2763 16379774 16382533 0.000000e+00 4152
22 TraesCS7D01G032300 chr7A 93.091 2417 154 7 2158 4564 15822539 15820126 0.000000e+00 3526
23 TraesCS7D01G032300 chr7A 91.304 1587 123 12 591 2167 15834334 15832753 0.000000e+00 2152
24 TraesCS7D01G032300 chr7A 95.185 1267 37 5 3847 5110 16393096 16394341 0.000000e+00 1980
25 TraesCS7D01G032300 chr7A 97.414 464 11 1 4647 5110 16317407 16317869 0.000000e+00 789
26 TraesCS7D01G032300 chr7B 93.994 2564 131 12 2563 5110 655811491 655814047 0.000000e+00 3860
27 TraesCS7D01G032300 chr7B 93.419 2583 140 18 1 2571 655806556 655809120 0.000000e+00 3801


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 TraesCS7D01G032300 chr7D 16757619 16762728 5109 True 9437.000000 9437 100.000000 1 5110 1 chr7D.!!$R1 5109
1 TraesCS7D01G032300 chr7D 17119884 17124964 5080 False 4054.500000 7758 94.607000 1 5110 2 chr7D.!!$F2 5109
2 TraesCS7D01G032300 chr7D 16993323 16996489 3166 False 1709.333333 3960 97.044000 1 5110 3 chr7D.!!$F1 5109
3 TraesCS7D01G032300 chr4A 717257430 717262521 5091 True 8080.000000 8080 95.281000 1 5110 1 chr4A.!!$R2 5109
4 TraesCS7D01G032300 chr4A 717284190 717287668 3478 True 2744.000000 4743 95.657000 1207 4668 2 chr4A.!!$R4 3461
5 TraesCS7D01G032300 chr4A 717801702 717806871 5169 False 2692.000000 5559 95.486667 1 5110 3 chr4A.!!$F2 5109
6 TraesCS7D01G032300 chr4A 717750998 717756019 5021 False 2633.000000 7084 94.110667 1 5110 3 chr4A.!!$F1 5109
7 TraesCS7D01G032300 chr4A 717222253 717225661 3408 True 1795.333333 4004 94.627333 1757 5110 3 chr4A.!!$R3 3353
8 TraesCS7D01G032300 chr4A 717234750 717235527 777 True 1203.000000 1203 94.602000 1 776 1 chr4A.!!$R1 775
9 TraesCS7D01G032300 chr7A 16424946 16430025 5079 False 7731.000000 7731 94.090000 1 5110 1 chr7A.!!$F3 5109
10 TraesCS7D01G032300 chr7A 16379774 16382533 2759 False 4152.000000 4152 93.847000 2 2763 1 chr7A.!!$F1 2761
11 TraesCS7D01G032300 chr7A 16312851 16317869 5018 False 3687.500000 6586 96.092000 1 5110 2 chr7A.!!$F4 5109
12 TraesCS7D01G032300 chr7A 15820126 15822539 2413 True 3526.000000 3526 93.091000 2158 4564 1 chr7A.!!$R1 2406
13 TraesCS7D01G032300 chr7A 15832753 15834334 1581 True 2152.000000 2152 91.304000 591 2167 1 chr7A.!!$R2 1576
14 TraesCS7D01G032300 chr7A 16393096 16394341 1245 False 1980.000000 1980 95.185000 3847 5110 1 chr7A.!!$F2 1263
15 TraesCS7D01G032300 chr7B 655806556 655814047 7491 False 3830.500000 3860 93.706500 1 5110 2 chr7B.!!$F1 5109

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
723 733 0.322975 CAGCACTCCCAGCTTAGTGT 59.677 55.0 17.50 2.88 44.03 3.55 F
1489 1626 0.541863 CGAGGCCCCAACAGTTCTAT 59.458 55.0 0.00 0.00 0.00 1.98 F
2689 5226 0.329596 GGTGGAGACAAGAGCCCAAT 59.670 55.0 0.00 0.00 46.06 3.16 F
3279 5820 0.740516 GACAAGCTCAGCTGGCTCTC 60.741 60.0 24.11 18.42 39.62 3.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1895 2036 1.078143 GCGGAGGTGATTCAAGGCT 60.078 57.895 0.00 0.00 0.00 4.58 R
3147 5688 1.160137 GCGATGACTGCAAGAAGGTT 58.840 50.000 0.00 0.00 37.43 3.50 R
3807 6348 1.004745 GTCAATGGAGAAGGCTTCCCA 59.995 52.381 28.14 28.14 35.46 4.37 R
4966 7610 0.679960 GCGGCAATTACAAGGGACCT 60.680 55.000 0.00 0.00 0.00 3.85 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
39 41 1.457346 GAGAGCCAATGGACTTGTGG 58.543 55.000 2.05 0.00 32.61 4.17
132 134 8.871686 ACATTTGAACAATCCAAAGAAGTAAC 57.128 30.769 0.00 0.00 37.00 2.50
191 195 6.186420 TCTTTAGCTGCATGGGTCATATAA 57.814 37.500 1.02 0.00 0.00 0.98
214 218 4.524316 TTTCAATCCAATCCTTGCACAG 57.476 40.909 0.00 0.00 0.00 3.66
257 261 5.873179 TCGACTAAAATTCGAGGCAAAAT 57.127 34.783 0.00 0.00 40.51 1.82
363 371 1.973281 ATGGGGCGAGCAGTGTTTG 60.973 57.895 0.00 0.00 0.00 2.93
381 389 9.065871 CAGTGTTTGCTAAATAATAAAGAGCAC 57.934 33.333 0.00 0.00 42.56 4.40
668 678 3.068165 TGAGTACTGCTTATCATGGACCG 59.932 47.826 0.00 0.00 0.00 4.79
671 681 3.845781 ACTGCTTATCATGGACCGAAT 57.154 42.857 0.00 0.00 0.00 3.34
723 733 0.322975 CAGCACTCCCAGCTTAGTGT 59.677 55.000 17.50 2.88 44.03 3.55
727 737 2.758979 GCACTCCCAGCTTAGTGTAGTA 59.241 50.000 17.50 0.00 44.03 1.82
810 820 3.760684 ACTGGAAGGATTTCACATTGCTC 59.239 43.478 0.00 0.00 39.30 4.26
854 868 1.908619 TGCAGCCATAGAGGAAAGTGA 59.091 47.619 0.00 0.00 41.22 3.41
855 869 2.284190 GCAGCCATAGAGGAAAGTGAC 58.716 52.381 0.00 0.00 41.22 3.67
1265 1388 3.317406 TGTACCTCAGGTCATATGGCAT 58.683 45.455 9.98 4.88 37.09 4.40
1324 1453 1.322538 GCACCCTTGCCCTTACCATG 61.323 60.000 0.00 0.00 43.66 3.66
1489 1626 0.541863 CGAGGCCCCAACAGTTCTAT 59.458 55.000 0.00 0.00 0.00 1.98
1622 1761 3.041946 ACCTCCATTACCCTCACTCATC 58.958 50.000 0.00 0.00 0.00 2.92
1665 1804 3.006110 CCCTTGTAACTAGGTGTCGTCAA 59.994 47.826 0.00 0.00 0.00 3.18
1718 1857 1.528292 GCATTTACCCAACACCGCCA 61.528 55.000 0.00 0.00 0.00 5.69
1721 1860 2.321263 TTTACCCAACACCGCCACGA 62.321 55.000 0.00 0.00 0.00 4.35
1732 1871 1.667830 CGCCACGATGTTCACCAGT 60.668 57.895 0.00 0.00 0.00 4.00
1794 1933 4.365514 TCTTATCTTTGTGGTGCTTGGA 57.634 40.909 0.00 0.00 0.00 3.53
1895 2036 3.541224 GACTCATGGAGGAGGCCTA 57.459 57.895 4.42 0.00 36.92 3.93
2413 2571 2.834505 CCGCCATCACCCCATTGG 60.835 66.667 0.00 0.00 41.37 3.16
2592 5129 7.956328 ACCACTATCAGTGTAGAACAATCTA 57.044 36.000 5.65 0.00 44.50 1.98
2619 5156 8.500773 AGAATTTGAATATTGCTTGCACTTTTG 58.499 29.630 0.00 0.00 0.00 2.44
2624 5161 9.486497 TTGAATATTGCTTGCACTTTTGAATTA 57.514 25.926 0.00 0.00 0.00 1.40
2689 5226 0.329596 GGTGGAGACAAGAGCCCAAT 59.670 55.000 0.00 0.00 46.06 3.16
2988 5529 5.695816 TGCTAAAATTGTTGTCCTTTCATGC 59.304 36.000 0.00 0.00 0.00 4.06
3159 5700 3.390135 TCAACTCGTAACCTTCTTGCAG 58.610 45.455 0.00 0.00 0.00 4.41
3279 5820 0.740516 GACAAGCTCAGCTGGCTCTC 60.741 60.000 24.11 18.42 39.62 3.20
3326 5867 7.907389 TCATTGATCCTGTATATCCAAGTACC 58.093 38.462 0.00 0.00 0.00 3.34
3397 5938 5.937540 TCGTCAAATGTTCTTATGGTCATGT 59.062 36.000 0.00 0.00 0.00 3.21
3413 5954 4.572389 GGTCATGTGATTTTCTGCTACGAT 59.428 41.667 0.00 0.00 0.00 3.73
3434 5975 6.441924 ACGATAGATCCCTTGTCATTATGGAT 59.558 38.462 0.00 0.00 38.50 3.41
3732 6273 6.155221 TGAGGTACTAAGAGTTGATTGCAGAT 59.845 38.462 0.00 0.00 41.55 2.90
3807 6348 4.217983 CACTTCTCCTACTTGGTCGTAACT 59.782 45.833 0.00 0.00 37.07 2.24
3930 6471 1.272490 CTGGACAGCCACGACTCTTAA 59.728 52.381 0.00 0.00 39.92 1.85
4094 6635 2.139118 GCTCGCAATCCTACATCCTTC 58.861 52.381 0.00 0.00 0.00 3.46
4129 6671 1.969809 GATCGTGTCATTGCAGCGCA 61.970 55.000 11.47 0.00 36.47 6.09
4185 6734 5.278315 GGACTTTTTGTCGCTATGTTCCTTT 60.278 40.000 0.00 0.00 46.24 3.11
4246 6851 2.380064 AATCTCTGTTTGCCACCCAA 57.620 45.000 0.00 0.00 0.00 4.12
4351 6957 5.884792 AGAGATAAGGGTTTGCATCTTGAAG 59.115 40.000 0.00 0.00 0.00 3.02
4789 7403 9.276590 CCAAGCTATGTTCTCAATATTCACATA 57.723 33.333 0.00 0.00 30.70 2.29
4988 7632 0.326595 TCCCTTGTAATTGCCGCAGA 59.673 50.000 0.00 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 41 0.179081 GGGGCGATGAGTAAGGACAC 60.179 60.000 0.00 0.00 0.00 3.67
132 134 1.600636 TGGTTCAAGCGCTTCCCAG 60.601 57.895 22.21 9.49 0.00 4.45
214 218 4.917415 CGATCATGGAAAGGTTCACAAAAC 59.083 41.667 0.00 0.00 0.00 2.43
256 260 1.002857 CCAACCCCAGAAGGAGGAAT 58.997 55.000 0.00 0.00 38.24 3.01
257 261 0.402861 ACCAACCCCAGAAGGAGGAA 60.403 55.000 0.00 0.00 38.24 3.36
363 371 7.291567 CGGCTAAGTGCTCTTTATTATTTAGC 58.708 38.462 6.31 6.71 40.39 3.09
495 504 6.239232 GGAGCCTCGGTGTCTCTAAATTAATA 60.239 42.308 0.00 0.00 0.00 0.98
500 509 1.757699 GGAGCCTCGGTGTCTCTAAAT 59.242 52.381 0.00 0.00 0.00 1.40
525 534 6.986231 GGGAGGTTAATGCCTATCAAAATTTG 59.014 38.462 0.00 0.00 39.34 2.32
526 535 6.902974 AGGGAGGTTAATGCCTATCAAAATTT 59.097 34.615 0.00 0.00 39.59 1.82
668 678 5.684704 TGGTCCTGGACATGAAAGATATTC 58.315 41.667 26.94 6.56 33.68 1.75
671 681 5.222027 TGTTTGGTCCTGGACATGAAAGATA 60.222 40.000 26.94 9.72 33.68 1.98
723 733 3.042682 TGAAATCCCTGGCCGATTACTA 58.957 45.455 0.00 0.00 29.78 1.82
727 737 0.625849 ACTGAAATCCCTGGCCGATT 59.374 50.000 0.00 0.00 0.00 3.34
810 820 0.321122 GGAGACAGACCAAGGTGCAG 60.321 60.000 0.00 0.00 0.00 4.41
854 868 2.837591 TGGTACACACATATGCTCCAGT 59.162 45.455 1.58 0.00 0.00 4.00
855 869 3.541996 TGGTACACACATATGCTCCAG 57.458 47.619 1.58 0.00 0.00 3.86
1163 1181 4.096682 CCTAAGGAGTAAGGAAGACGTCAG 59.903 50.000 19.50 0.43 34.58 3.51
1324 1453 3.365832 CGCCAGAATTGTATTGTGCATC 58.634 45.455 0.00 0.00 0.00 3.91
1489 1626 3.300388 AGGAGAAATGAGTCGCCTGATA 58.700 45.455 0.00 0.00 45.10 2.15
1622 1761 1.699634 TCCTGGTCTGAACAAGAAGGG 59.300 52.381 0.00 0.00 34.69 3.95
1665 1804 4.950050 CAGTGAGTCTGGTAGTGAGTTTT 58.050 43.478 0.00 0.00 40.23 2.43
1718 1857 3.401033 TCAATCACTGGTGAACATCGT 57.599 42.857 7.53 0.00 43.58 3.73
1721 1860 5.319453 AGTTGATCAATCACTGGTGAACAT 58.681 37.500 12.12 0.71 43.58 2.71
1732 1871 5.500234 CCAGGGAAGTAAGTTGATCAATCA 58.500 41.667 12.12 0.00 34.44 2.57
1794 1933 2.615493 CCTGGAGCCAGTAACACGAAAT 60.615 50.000 14.97 0.00 42.15 2.17
1895 2036 1.078143 GCGGAGGTGATTCAAGGCT 60.078 57.895 0.00 0.00 0.00 4.58
2413 2571 3.462678 GTCAGAGGAGGTCGCCCC 61.463 72.222 0.00 0.00 0.00 5.80
2592 5129 8.611654 AAAGTGCAAGCAATATTCAAATTCTT 57.388 26.923 0.00 0.00 0.00 2.52
2600 5137 8.924691 TGTAATTCAAAAGTGCAAGCAATATTC 58.075 29.630 0.00 0.00 0.00 1.75
2624 5161 8.309163 ACGCAATAAATTTCATCAACATTTGT 57.691 26.923 0.00 0.00 0.00 2.83
2942 5482 8.668510 AGCAATGGACTTGAGTTAACTATATG 57.331 34.615 8.42 5.98 36.97 1.78
2988 5529 6.034591 CAGCTTCAAATTCTGCATTAAGGAG 58.965 40.000 0.00 0.00 36.96 3.69
3147 5688 1.160137 GCGATGACTGCAAGAAGGTT 58.840 50.000 0.00 0.00 37.43 3.50
3159 5700 2.650813 CTAGGGCAGGTGGCGATGAC 62.651 65.000 0.00 0.00 46.16 3.06
3279 5820 2.353011 GCTCCCATGTGTTTCCAATGTG 60.353 50.000 0.00 0.00 0.00 3.21
3326 5867 2.604174 GGTCAAGCGACACAACGGG 61.604 63.158 0.00 0.00 44.54 5.28
3397 5938 5.540337 AGGGATCTATCGTAGCAGAAAATCA 59.460 40.000 0.00 0.00 0.00 2.57
3413 5954 6.745190 GCACATCCATAATGACAAGGGATCTA 60.745 42.308 0.00 0.00 36.24 1.98
3449 5990 2.594592 GGTGGAGCTGCAACCGTT 60.595 61.111 13.07 0.00 0.00 4.44
3732 6273 6.614694 AAGCACGTATGGGTCCATATAATA 57.385 37.500 12.29 0.00 40.49 0.98
3807 6348 1.004745 GTCAATGGAGAAGGCTTCCCA 59.995 52.381 28.14 28.14 35.46 4.37
4094 6635 1.506493 GATCTCATACCCAAGCTGCG 58.494 55.000 0.00 0.00 0.00 5.18
4129 6671 2.418628 CCAACGACAACAAGACAACTGT 59.581 45.455 0.00 0.00 0.00 3.55
4185 6734 2.409975 CGTCAAAGGAGCGGAAACTAA 58.590 47.619 0.00 0.00 0.00 2.24
4246 6851 3.737559 TTTGCCTCCAGGAATGTACAT 57.262 42.857 1.41 1.41 37.39 2.29
4351 6957 4.143986 AGACCCAAGAAGCTAGTATTGC 57.856 45.455 0.00 0.00 0.00 3.56
4789 7403 2.269023 TGACAGTCTCATTGGGTGGAT 58.731 47.619 1.31 0.00 0.00 3.41
4966 7610 0.679960 GCGGCAATTACAAGGGACCT 60.680 55.000 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.