Multiple sequence alignment - TraesCS4B01G303900

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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 TraesCS4B01G303900 chr4B 100.000 3176 0 0 1 3176 592080600 592077425 0.000000e+00 5866.0
1 TraesCS4B01G303900 chr4B 97.609 2384 41 5 793 3176 592188244 592185877 0.000000e+00 4072.0
2 TraesCS4B01G303900 chr4B 96.110 1234 47 1 943 2176 591955114 591953882 0.000000e+00 2012.0
3 TraesCS4B01G303900 chr4B 90.753 1341 111 6 864 2193 591909494 591908156 0.000000e+00 1777.0
4 TraesCS4B01G303900 chr4B 98.734 711 8 1 1 711 591956838 591956129 0.000000e+00 1262.0
5 TraesCS4B01G303900 chr4B 98.765 162 2 0 793 954 591956131 591955970 4.010000e-74 289.0
6 TraesCS4B01G303900 chr4A 94.293 1612 73 6 793 2388 677989075 677987467 0.000000e+00 2449.0
7 TraesCS4B01G303900 chr4A 93.298 1328 78 6 858 2177 677969659 677968335 0.000000e+00 1949.0
8 TraesCS4B01G303900 chr4A 90.971 1329 102 10 864 2180 677958660 677957338 0.000000e+00 1773.0
9 TraesCS4B01G303900 chr4A 84.379 717 93 11 5 711 677976703 677975996 0.000000e+00 686.0
10 TraesCS4B01G303900 chr4A 95.098 102 3 2 693 794 681667432 681667333 3.280000e-35 159.0
11 TraesCS4B01G303900 chr4A 93.651 63 4 0 602 664 677990561 677990499 9.380000e-16 95.3
12 TraesCS4B01G303900 chr4D 95.159 1384 67 0 793 2176 470138569 470137186 0.000000e+00 2185.0
13 TraesCS4B01G303900 chr4D 92.991 1384 84 3 793 2176 470130527 470129157 0.000000e+00 2006.0
14 TraesCS4B01G303900 chr4D 90.841 1332 101 13 864 2180 470121982 470120657 0.000000e+00 1764.0
15 TraesCS4B01G303900 chrUn 83.253 621 75 21 2496 3105 8041854 8042456 7.750000e-151 544.0
16 TraesCS4B01G303900 chrUn 83.253 621 75 21 2496 3105 448651186 448650584 7.750000e-151 544.0
17 TraesCS4B01G303900 chrUn 82.931 621 77 21 2496 3105 8038981 8039583 1.680000e-147 532.0
18 TraesCS4B01G303900 chr1B 83.253 621 75 21 2496 3105 632904738 632905340 7.750000e-151 544.0
19 TraesCS4B01G303900 chr1B 83.092 621 76 21 2496 3105 632907612 632908214 3.600000e-149 538.0
20 TraesCS4B01G303900 chr1B 83.092 621 76 21 2496 3105 632910486 632911088 3.600000e-149 538.0
21 TraesCS4B01G303900 chr1B 82.931 621 77 21 2496 3105 632892130 632892732 1.680000e-147 532.0
22 TraesCS4B01G303900 chr1B 82.448 621 80 22 2496 3105 632913360 632913962 1.690000e-142 516.0
23 TraesCS4B01G303900 chr1B 96.809 94 3 0 709 802 102141253 102141160 1.180000e-34 158.0
24 TraesCS4B01G303900 chr1B 96.809 94 3 0 701 794 498863934 498863841 1.180000e-34 158.0
25 TraesCS4B01G303900 chr3B 96.809 94 3 0 709 802 175772670 175772577 1.180000e-34 158.0
26 TraesCS4B01G303900 chr3B 96.809 94 3 0 709 802 175773985 175773892 1.180000e-34 158.0
27 TraesCS4B01G303900 chr3A 95.918 98 3 1 709 806 310784271 310784175 1.180000e-34 158.0
28 TraesCS4B01G303900 chr3A 94.898 98 4 1 701 797 550395305 550395208 5.490000e-33 152.0
29 TraesCS4B01G303900 chr6B 96.774 93 3 0 709 801 369484922 369484830 4.240000e-34 156.0
30 TraesCS4B01G303900 chr2B 95.833 96 3 1 709 804 383927841 383927935 1.530000e-33 154.0
31 TraesCS4B01G303900 chr2B 86.916 107 14 0 3066 3172 784202379 784202485 1.550000e-23 121.0


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 TraesCS4B01G303900 chr4B 592077425 592080600 3175 True 5866.000000 5866 100.000000 1 3176 1 chr4B.!!$R2 3175
1 TraesCS4B01G303900 chr4B 592185877 592188244 2367 True 4072.000000 4072 97.609000 793 3176 1 chr4B.!!$R3 2383
2 TraesCS4B01G303900 chr4B 591908156 591909494 1338 True 1777.000000 1777 90.753000 864 2193 1 chr4B.!!$R1 1329
3 TraesCS4B01G303900 chr4B 591953882 591956838 2956 True 1187.666667 2012 97.869667 1 2176 3 chr4B.!!$R4 2175
4 TraesCS4B01G303900 chr4A 677968335 677969659 1324 True 1949.000000 1949 93.298000 858 2177 1 chr4A.!!$R2 1319
5 TraesCS4B01G303900 chr4A 677957338 677958660 1322 True 1773.000000 1773 90.971000 864 2180 1 chr4A.!!$R1 1316
6 TraesCS4B01G303900 chr4A 677987467 677990561 3094 True 1272.150000 2449 93.972000 602 2388 2 chr4A.!!$R5 1786
7 TraesCS4B01G303900 chr4A 677975996 677976703 707 True 686.000000 686 84.379000 5 711 1 chr4A.!!$R3 706
8 TraesCS4B01G303900 chr4D 470137186 470138569 1383 True 2185.000000 2185 95.159000 793 2176 1 chr4D.!!$R3 1383
9 TraesCS4B01G303900 chr4D 470129157 470130527 1370 True 2006.000000 2006 92.991000 793 2176 1 chr4D.!!$R2 1383
10 TraesCS4B01G303900 chr4D 470120657 470121982 1325 True 1764.000000 1764 90.841000 864 2180 1 chr4D.!!$R1 1316
11 TraesCS4B01G303900 chrUn 448650584 448651186 602 True 544.000000 544 83.253000 2496 3105 1 chrUn.!!$R1 609
12 TraesCS4B01G303900 chrUn 8038981 8042456 3475 False 538.000000 544 83.092000 2496 3105 2 chrUn.!!$F1 609
13 TraesCS4B01G303900 chr1B 632904738 632913962 9224 False 534.000000 544 82.971250 2496 3105 4 chr1B.!!$F2 609
14 TraesCS4B01G303900 chr1B 632892130 632892732 602 False 532.000000 532 82.931000 2496 3105 1 chr1B.!!$F1 609

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 2104 1.076677 ACTCTTACTCCCTCCGTTCCA 59.923 52.381 0.0 0.0 0.00 3.53 F
1926 4192 0.915872 TCATGGGGCTCATCACCTGT 60.916 55.000 0.0 0.0 32.92 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2104 4370 2.684843 GCAGCTGGTTCTTCTGCGG 61.685 63.158 17.12 0.0 42.86 5.69 R
2876 13788 0.036577 CAGACTGCCACTGAAGGAGG 60.037 60.000 0.00 0.0 37.54 4.30 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
96 97 6.597280 GCATCACATTCTTCTCCTAGAAACTT 59.403 38.462 0.00 0.0 37.66 2.66
343 345 2.041081 TGGGACATCATTTCTTCCGGTT 59.959 45.455 0.00 0.0 0.00 4.44
360 362 2.290323 CGGTTTCCCTTCCATCTCTGTT 60.290 50.000 0.00 0.0 0.00 3.16
714 2095 5.963594 AGTTCATCGTTAACTCTTACTCCC 58.036 41.667 3.71 0.0 31.56 4.30
715 2096 5.715753 AGTTCATCGTTAACTCTTACTCCCT 59.284 40.000 3.71 0.0 31.56 4.20
716 2097 5.831702 TCATCGTTAACTCTTACTCCCTC 57.168 43.478 3.71 0.0 0.00 4.30
717 2098 4.643784 TCATCGTTAACTCTTACTCCCTCC 59.356 45.833 3.71 0.0 0.00 4.30
718 2099 3.012518 TCGTTAACTCTTACTCCCTCCG 58.987 50.000 3.71 0.0 0.00 4.63
719 2100 2.751806 CGTTAACTCTTACTCCCTCCGT 59.248 50.000 3.71 0.0 0.00 4.69
720 2101 3.192212 CGTTAACTCTTACTCCCTCCGTT 59.808 47.826 3.71 0.0 0.00 4.44
721 2102 4.673841 CGTTAACTCTTACTCCCTCCGTTC 60.674 50.000 3.71 0.0 0.00 3.95
722 2103 1.849977 ACTCTTACTCCCTCCGTTCC 58.150 55.000 0.00 0.0 0.00 3.62
723 2104 1.076677 ACTCTTACTCCCTCCGTTCCA 59.923 52.381 0.00 0.0 0.00 3.53
724 2105 2.176889 CTCTTACTCCCTCCGTTCCAA 58.823 52.381 0.00 0.0 0.00 3.53
725 2106 2.565834 CTCTTACTCCCTCCGTTCCAAA 59.434 50.000 0.00 0.0 0.00 3.28
726 2107 2.974099 TCTTACTCCCTCCGTTCCAAAA 59.026 45.455 0.00 0.0 0.00 2.44
727 2108 3.585732 TCTTACTCCCTCCGTTCCAAAAT 59.414 43.478 0.00 0.0 0.00 1.82
728 2109 4.778958 TCTTACTCCCTCCGTTCCAAAATA 59.221 41.667 0.00 0.0 0.00 1.40
729 2110 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.0 0.00 1.73
730 2111 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.0 0.00 1.98
731 2112 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.0 0.00 1.98
732 2113 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.0 0.00 2.90
733 2114 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.0 0.00 2.92
734 2115 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.0 0.00 3.06
735 2116 4.384208 CCCTCCGTTCCAAAATAGATGACT 60.384 45.833 0.00 0.0 0.00 3.41
736 2117 4.811557 CCTCCGTTCCAAAATAGATGACTC 59.188 45.833 0.00 0.0 0.00 3.36
737 2118 5.414789 TCCGTTCCAAAATAGATGACTCA 57.585 39.130 0.00 0.0 0.00 3.41
738 2119 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.0 0.00 3.02
739 2120 5.642063 TCCGTTCCAAAATAGATGACTCAAC 59.358 40.000 0.00 0.0 0.00 3.18
740 2121 5.643777 CCGTTCCAAAATAGATGACTCAACT 59.356 40.000 0.00 0.0 0.00 3.16
741 2122 6.149474 CCGTTCCAAAATAGATGACTCAACTT 59.851 38.462 0.00 0.0 0.00 2.66
742 2123 7.308589 CCGTTCCAAAATAGATGACTCAACTTT 60.309 37.037 0.00 0.0 0.00 2.66
743 2124 7.535258 CGTTCCAAAATAGATGACTCAACTTTG 59.465 37.037 0.00 0.0 0.00 2.77
744 2125 8.352942 GTTCCAAAATAGATGACTCAACTTTGT 58.647 33.333 0.00 0.0 0.00 2.83
745 2126 9.567776 TTCCAAAATAGATGACTCAACTTTGTA 57.432 29.630 0.00 0.0 0.00 2.41
746 2127 8.999431 TCCAAAATAGATGACTCAACTTTGTAC 58.001 33.333 0.00 0.0 0.00 2.90
747 2128 9.003658 CCAAAATAGATGACTCAACTTTGTACT 57.996 33.333 0.00 0.0 0.00 2.73
784 2165 9.746711 CAAAGTTGAGTCATCTATTTTAGAACG 57.253 33.333 4.14 0.0 38.50 3.95
785 2166 8.480643 AAGTTGAGTCATCTATTTTAGAACGG 57.519 34.615 4.14 0.0 38.50 4.44
786 2167 7.837863 AGTTGAGTCATCTATTTTAGAACGGA 58.162 34.615 1.70 0.0 38.50 4.69
787 2168 7.976734 AGTTGAGTCATCTATTTTAGAACGGAG 59.023 37.037 1.70 0.0 38.50 4.63
788 2169 6.806751 TGAGTCATCTATTTTAGAACGGAGG 58.193 40.000 0.00 0.0 38.50 4.30
789 2170 6.163135 AGTCATCTATTTTAGAACGGAGGG 57.837 41.667 0.00 0.0 38.50 4.30
790 2171 5.897824 AGTCATCTATTTTAGAACGGAGGGA 59.102 40.000 0.00 0.0 38.50 4.20
791 2172 6.041069 AGTCATCTATTTTAGAACGGAGGGAG 59.959 42.308 0.00 0.0 38.50 4.30
823 2204 5.236425 ACTTCCCTCCTCCTTCCTTTATA 57.764 43.478 0.00 0.0 0.00 0.98
1926 4192 0.915872 TCATGGGGCTCATCACCTGT 60.916 55.000 0.00 0.0 32.92 4.00
2292 4580 9.793259 TTCATTCTAGGTAACACAGAGAAAATT 57.207 29.630 0.00 0.0 41.41 1.82
2455 4743 3.119424 TGACTTCAAACGGGGTTTCAAAC 60.119 43.478 0.00 0.0 33.10 2.93
2874 13786 1.760480 GCTGTCCTCCTCCTCCTCC 60.760 68.421 0.00 0.0 0.00 4.30
2875 13787 2.015081 CTGTCCTCCTCCTCCTCCT 58.985 63.158 0.00 0.0 0.00 3.69
2876 13788 0.106217 CTGTCCTCCTCCTCCTCCTC 60.106 65.000 0.00 0.0 0.00 3.71
3006 13942 1.812922 CACATCAGCCGCCTCTGTC 60.813 63.158 0.54 0.0 35.63 3.51
3007 13943 2.285773 ACATCAGCCGCCTCTGTCA 61.286 57.895 0.54 0.0 35.63 3.58
3111 16921 2.043752 TCTGCCCGACCGGTGATA 60.044 61.111 14.63 0.0 0.00 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
96 97 3.239464 TGGCACAAGGCTGAGTCA 58.761 55.556 0.00 0.00 44.01 3.41
343 345 3.251484 AGACAACAGAGATGGAAGGGAA 58.749 45.455 0.00 0.00 0.00 3.97
360 362 2.364972 TCTCATGGCGGAGATAGACA 57.635 50.000 4.75 0.00 38.95 3.41
547 549 3.071479 TCCAAACTTCACAATAGCCGTC 58.929 45.455 0.00 0.00 0.00 4.79
706 2087 3.412237 TTTTGGAACGGAGGGAGTAAG 57.588 47.619 0.00 0.00 0.00 2.34
708 2089 4.355549 TCTATTTTGGAACGGAGGGAGTA 58.644 43.478 0.00 0.00 0.00 2.59
709 2090 3.178865 TCTATTTTGGAACGGAGGGAGT 58.821 45.455 0.00 0.00 0.00 3.85
710 2091 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
711 2092 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
712 2093 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
713 2094 4.770795 AGTCATCTATTTTGGAACGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
714 2095 5.419542 TGAGTCATCTATTTTGGAACGGAG 58.580 41.667 0.00 0.00 0.00 4.63
715 2096 5.414789 TGAGTCATCTATTTTGGAACGGA 57.585 39.130 0.00 0.00 0.00 4.69
716 2097 5.643777 AGTTGAGTCATCTATTTTGGAACGG 59.356 40.000 1.70 0.00 0.00 4.44
717 2098 6.727824 AGTTGAGTCATCTATTTTGGAACG 57.272 37.500 1.70 0.00 0.00 3.95
718 2099 8.352942 ACAAAGTTGAGTCATCTATTTTGGAAC 58.647 33.333 14.35 0.00 40.00 3.62
719 2100 8.463930 ACAAAGTTGAGTCATCTATTTTGGAA 57.536 30.769 14.35 0.00 40.00 3.53
720 2101 8.999431 GTACAAAGTTGAGTCATCTATTTTGGA 58.001 33.333 14.35 6.88 40.00 3.53
721 2102 9.003658 AGTACAAAGTTGAGTCATCTATTTTGG 57.996 33.333 14.35 0.00 40.00 3.28
758 2139 9.746711 CGTTCTAAAATAGATGACTCAACTTTG 57.253 33.333 0.00 0.00 34.22 2.77
759 2140 8.936864 CCGTTCTAAAATAGATGACTCAACTTT 58.063 33.333 0.00 0.00 34.22 2.66
760 2141 8.311836 TCCGTTCTAAAATAGATGACTCAACTT 58.688 33.333 0.00 0.00 34.22 2.66
761 2142 7.837863 TCCGTTCTAAAATAGATGACTCAACT 58.162 34.615 0.00 0.00 34.22 3.16
762 2143 7.222999 CCTCCGTTCTAAAATAGATGACTCAAC 59.777 40.741 0.00 0.00 34.22 3.18
763 2144 7.265673 CCTCCGTTCTAAAATAGATGACTCAA 58.734 38.462 0.00 0.00 34.22 3.02
764 2145 6.183360 CCCTCCGTTCTAAAATAGATGACTCA 60.183 42.308 0.00 0.00 34.22 3.41
765 2146 6.040616 TCCCTCCGTTCTAAAATAGATGACTC 59.959 42.308 0.00 0.00 34.22 3.36
766 2147 5.897824 TCCCTCCGTTCTAAAATAGATGACT 59.102 40.000 0.00 0.00 34.22 3.41
767 2148 6.158023 TCCCTCCGTTCTAAAATAGATGAC 57.842 41.667 0.00 0.00 34.22 3.06
768 2149 5.897824 ACTCCCTCCGTTCTAAAATAGATGA 59.102 40.000 0.00 0.00 34.22 2.92
769 2150 6.163135 ACTCCCTCCGTTCTAAAATAGATG 57.837 41.667 0.00 0.00 34.22 2.90
770 2151 6.016443 CGTACTCCCTCCGTTCTAAAATAGAT 60.016 42.308 0.00 0.00 34.22 1.98
771 2152 5.297776 CGTACTCCCTCCGTTCTAAAATAGA 59.702 44.000 0.00 0.00 0.00 1.98
772 2153 5.067023 ACGTACTCCCTCCGTTCTAAAATAG 59.933 44.000 0.00 0.00 0.00 1.73
773 2154 4.949856 ACGTACTCCCTCCGTTCTAAAATA 59.050 41.667 0.00 0.00 0.00 1.40
774 2155 3.766051 ACGTACTCCCTCCGTTCTAAAAT 59.234 43.478 0.00 0.00 0.00 1.82
775 2156 3.057315 CACGTACTCCCTCCGTTCTAAAA 60.057 47.826 0.00 0.00 31.46 1.52
776 2157 2.489329 CACGTACTCCCTCCGTTCTAAA 59.511 50.000 0.00 0.00 31.46 1.85
777 2158 2.086869 CACGTACTCCCTCCGTTCTAA 58.913 52.381 0.00 0.00 31.46 2.10
778 2159 1.003580 ACACGTACTCCCTCCGTTCTA 59.996 52.381 0.00 0.00 31.46 2.10
779 2160 0.251077 ACACGTACTCCCTCCGTTCT 60.251 55.000 0.00 0.00 31.46 3.01
780 2161 0.109412 CACACGTACTCCCTCCGTTC 60.109 60.000 0.00 0.00 31.46 3.95
781 2162 0.825010 ACACACGTACTCCCTCCGTT 60.825 55.000 0.00 0.00 31.46 4.44
782 2163 0.036732 TACACACGTACTCCCTCCGT 59.963 55.000 0.00 0.00 34.71 4.69
783 2164 0.449388 GTACACACGTACTCCCTCCG 59.551 60.000 0.00 0.00 43.97 4.63
2104 4370 2.684843 GCAGCTGGTTCTTCTGCGG 61.685 63.158 17.12 0.00 42.86 5.69
2292 4580 9.656040 TTTTTATTAACTCGATGGTAGCACTTA 57.344 29.630 0.00 0.00 0.00 2.24
2455 4743 9.914923 TTTTCGAATGAGATGTTTGTATATTCG 57.085 29.630 0.00 0.00 43.76 3.34
2557 7718 4.760047 GTCAGTGCCCGCGGACAT 62.760 66.667 30.73 8.78 34.51 3.06
2874 13786 0.248843 GACTGCCACTGAAGGAGGAG 59.751 60.000 0.00 0.00 0.00 3.69
2875 13787 0.178921 AGACTGCCACTGAAGGAGGA 60.179 55.000 0.00 0.00 0.00 3.71
2876 13788 0.036577 CAGACTGCCACTGAAGGAGG 60.037 60.000 0.00 0.00 37.54 4.30
3006 13942 2.180017 GCAGCTGAAATGGCGGTG 59.820 61.111 20.43 0.00 34.52 4.94
3007 13943 3.434319 CGCAGCTGAAATGGCGGT 61.434 61.111 20.43 0.00 45.27 5.68
3010 13946 0.041839 CGTATCGCAGCTGAAATGGC 60.042 55.000 20.43 0.00 0.00 4.40
3111 16921 1.270839 CCGGAACACCTGTCATTCACT 60.271 52.381 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.