Multiple sequence alignment - TraesCS3A01G261000

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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 TraesCS3A01G261000 chr3A 100.000 3025 0 0 1 3025 483920745 483923769 0.000000e+00 5587
1 TraesCS3A01G261000 chr3A 90.323 93 6 1 2403 2495 483923049 483923138 5.300000e-23 119
2 TraesCS3A01G261000 chr3A 90.323 93 6 1 2305 2394 483923147 483923239 5.300000e-23 119
3 TraesCS3A01G261000 chr3D 96.030 3048 72 22 2 3025 380450104 380453126 0.000000e+00 4913
4 TraesCS3A01G261000 chr3D 83.249 197 21 8 1 194 380450067 380450254 1.440000e-38 171
5 TraesCS3A01G261000 chr3D 91.398 93 5 3 2403 2495 380452418 380452507 1.140000e-24 124
6 TraesCS3A01G261000 chr3D 89.130 92 8 1 2305 2394 380452516 380452607 2.460000e-21 113
7 TraesCS3A01G261000 chr6B 80.093 216 37 4 2695 2907 64189267 64189479 4.040000e-34 156


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 TraesCS3A01G261000 chr3A 483920745 483923769 3024 False 1941.666667 5587 93.548667 1 3025 3 chr3A.!!$F1 3024
1 TraesCS3A01G261000 chr3D 380450067 380453126 3059 False 1330.250000 4913 89.951750 1 3025 4 chr3D.!!$F1 3024

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
930 967 0.239347 GCATACTCGGGCATGCATTC 59.761 55.0 21.36 7.43 45.51 2.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2427 2482 0.533755 AGTTATCATGGGCAGCGAGC 60.534 55.0 0.0 0.0 44.65 5.03 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
30 31 1.333177 GACTCGGCCAGTCCTCATAT 58.667 55.000 19.08 0.00 45.47 1.78
75 112 3.257393 CCAGTTCTCATACAGTCAGCAC 58.743 50.000 0.00 0.00 0.00 4.40
91 128 1.966762 CACCAATTCGGCCAGCTTT 59.033 52.632 2.24 0.00 39.03 3.51
109 146 3.058155 GCTTTCATATGATCAGCAGCAGG 60.058 47.826 23.41 4.21 33.34 4.85
259 296 2.362329 GATCTCCTCCGCCAGTCAGC 62.362 65.000 0.00 0.00 0.00 4.26
414 451 5.070001 CCAGTTCTTTGGACAATTGGTCTA 58.930 41.667 10.83 0.45 46.16 2.59
415 452 5.182001 CCAGTTCTTTGGACAATTGGTCTAG 59.818 44.000 10.83 0.89 46.16 2.43
489 526 2.107204 ACCAGAGCATGTTCTGAAGGTT 59.893 45.455 33.54 14.02 45.95 3.50
571 608 7.888250 AGATGGACCATTAAGGAAAAGATTC 57.112 36.000 8.78 0.00 41.22 2.52
611 648 6.882610 TTACAAAAAGCACATCAGATCAGT 57.117 33.333 0.00 0.00 0.00 3.41
677 714 4.657814 AGAGACAGAGAGAGGAAGAAGT 57.342 45.455 0.00 0.00 0.00 3.01
698 735 7.661847 AGAAGTTGGAATAAAGTCGTCTCAAAT 59.338 33.333 0.00 0.00 0.00 2.32
718 755 1.275010 TGGAAGCAGTGAAGCGACATA 59.725 47.619 0.00 0.00 40.15 2.29
722 759 2.766313 AGCAGTGAAGCGACATAAACA 58.234 42.857 0.00 0.00 40.15 2.83
828 865 3.960755 AGCTTGTGAGGGCTTTTAAGTTT 59.039 39.130 0.00 0.00 34.96 2.66
930 967 0.239347 GCATACTCGGGCATGCATTC 59.761 55.000 21.36 7.43 45.51 2.67
969 1006 5.538433 TGGAAGAACCTGGAAAGGTAAAATG 59.462 40.000 0.00 0.00 42.20 2.32
986 1023 6.531594 GGTAAAATGAAGACAAGGCATTTAGC 59.468 38.462 0.00 0.00 40.28 3.09
1035 1072 4.745620 GCTATCCTATTGAAGACGGTGAAC 59.254 45.833 0.00 0.00 0.00 3.18
1036 1073 4.819105 ATCCTATTGAAGACGGTGAACA 57.181 40.909 0.00 0.00 0.00 3.18
1041 1078 2.900716 TGAAGACGGTGAACATGACA 57.099 45.000 0.00 0.00 0.00 3.58
1042 1079 3.186702 TGAAGACGGTGAACATGACAA 57.813 42.857 0.00 0.00 0.00 3.18
1071 1108 0.740868 ACATGGCCGACGACATCTTG 60.741 55.000 0.00 0.00 0.00 3.02
1113 1150 2.569853 TCCATTGTACAGGATCAACGGT 59.430 45.455 0.00 0.00 30.39 4.83
1137 1174 8.208718 GTCATTTACCACAATACTATGCTGAA 57.791 34.615 0.00 0.00 0.00 3.02
1145 1182 8.432013 ACCACAATACTATGCTGAAATGATAGA 58.568 33.333 0.00 0.00 0.00 1.98
1161 1198 8.463930 AAATGATAGACAAACTGAAGAAACCA 57.536 30.769 0.00 0.00 0.00 3.67
1167 1204 4.340617 ACAAACTGAAGAAACCACCAAGA 58.659 39.130 0.00 0.00 0.00 3.02
1169 1206 4.983671 AACTGAAGAAACCACCAAGAAC 57.016 40.909 0.00 0.00 0.00 3.01
1178 1230 3.297134 ACCACCAAGAACACTGAATGT 57.703 42.857 0.00 0.00 46.42 2.71
1191 1243 6.174720 ACACTGAATGTTGAGGAACTAAGA 57.825 37.500 0.00 0.00 37.08 2.10
1298 1350 2.558359 CCTTGGACCTGGAATTTGACAC 59.442 50.000 0.00 0.00 0.00 3.67
1596 1651 3.956199 CTCACAAATTACAGGCCCATGAT 59.044 43.478 0.00 0.00 0.00 2.45
1605 1660 3.542304 GCCCATGATCCTTTGGCC 58.458 61.111 0.00 0.00 36.07 5.36
1710 1765 1.608717 CCCCTGTCTCACTTCTCCCG 61.609 65.000 0.00 0.00 0.00 5.14
1716 1771 1.544691 GTCTCACTTCTCCCGCACTTA 59.455 52.381 0.00 0.00 0.00 2.24
1756 1811 4.744795 ACATTAAATCAGGACGCTCTCT 57.255 40.909 0.00 0.00 0.00 3.10
1780 1835 5.357742 TCCTGCAATTATGTCTCAAGCTA 57.642 39.130 0.00 0.00 0.00 3.32
1932 1987 3.090952 TGTGCATTAAGGTGTTGTTGC 57.909 42.857 0.00 0.00 0.00 4.17
2022 2077 8.606830 ACCTCTTGTACAAAGAGAAGGATAAAT 58.393 33.333 24.62 6.06 44.96 1.40
2111 2166 9.820725 CCTTATGATATGATTCCTGAGAGATTC 57.179 37.037 0.00 0.00 0.00 2.52
2427 2482 2.107953 GCTAGCTGGGAGAAGGCG 59.892 66.667 7.70 0.00 0.00 5.52
2428 2483 2.107953 CTAGCTGGGAGAAGGCGC 59.892 66.667 0.00 0.00 0.00 6.53
2430 2485 2.362329 CTAGCTGGGAGAAGGCGCTC 62.362 65.000 7.64 0.00 32.49 5.03
2471 2526 9.593134 CTGATCAAGTTCTTTGTTAGCTAGTAT 57.407 33.333 0.00 0.00 38.01 2.12
2553 2608 5.951148 AGTCTCCTAGTTTAGTGGTACCTTC 59.049 44.000 14.36 6.51 0.00 3.46
2555 2610 4.019174 TCCTAGTTTAGTGGTACCTTCGG 58.981 47.826 14.36 2.05 0.00 4.30
2557 2612 1.904537 AGTTTAGTGGTACCTTCGGGG 59.095 52.381 14.36 0.00 40.03 5.73
2558 2613 1.901833 GTTTAGTGGTACCTTCGGGGA 59.098 52.381 14.36 0.00 40.03 4.81
2559 2614 1.856629 TTAGTGGTACCTTCGGGGAG 58.143 55.000 14.36 0.00 40.03 4.30
2560 2615 1.002069 TAGTGGTACCTTCGGGGAGA 58.998 55.000 14.36 0.00 40.03 3.71
2561 2616 0.115745 AGTGGTACCTTCGGGGAGAA 59.884 55.000 14.36 0.00 40.03 2.87
2627 2682 5.759059 TGATATCTTCTGGAAACCAAGCAT 58.241 37.500 3.98 0.00 30.80 3.79
2648 2703 5.520632 CATGATTGCCTCAGAAAATGCTAG 58.479 41.667 0.00 0.00 37.28 3.42
2762 2817 5.124617 CCTTTTTCTTTGAGGGATAGCAGTC 59.875 44.000 0.00 0.00 0.00 3.51
2932 2987 1.181786 GGGTGATTTTGGAATGCCGA 58.818 50.000 0.00 0.00 36.79 5.54
2964 3019 2.876955 CGCCGACGGTAGGTAACA 59.123 61.111 16.73 0.00 35.08 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 0.952497 GTTGCTGCTGCTGCTGACTA 60.952 55.000 27.67 8.50 40.01 2.59
75 112 0.819582 ATGAAAGCTGGCCGAATTGG 59.180 50.000 0.00 0.00 42.50 3.16
91 128 2.970640 AGACCTGCTGCTGATCATATGA 59.029 45.455 8.10 8.10 0.00 2.15
109 146 2.159028 GGGCCAGACTACTTGATGAGAC 60.159 54.545 4.39 0.00 0.00 3.36
192 229 2.688794 GGCTGTTGAGAGCTGCTGC 61.689 63.158 7.01 7.62 39.11 5.25
193 230 1.299562 CTGGCTGTTGAGAGCTGCTG 61.300 60.000 7.01 0.00 39.11 4.41
266 303 3.670637 GATGGGCTCTCGTGCTGCA 62.671 63.158 0.00 0.00 0.00 4.41
394 431 6.881602 AGATCTAGACCAATTGTCCAAAGAAC 59.118 38.462 4.43 5.28 45.68 3.01
414 451 0.549950 CAATGTGGGGAGGCAGATCT 59.450 55.000 0.00 0.00 0.00 2.75
415 452 0.548031 TCAATGTGGGGAGGCAGATC 59.452 55.000 0.00 0.00 0.00 2.75
489 526 1.032014 GCACTGTGCCTCTTTTTCCA 58.968 50.000 21.78 0.00 37.42 3.53
549 586 6.836007 GGAGAATCTTTTCCTTAATGGTCCAT 59.164 38.462 0.00 0.00 33.97 3.41
581 618 7.362662 TCTGATGTGCTTTTTGTAATCTTCAC 58.637 34.615 0.00 0.00 0.00 3.18
584 621 8.114331 TGATCTGATGTGCTTTTTGTAATCTT 57.886 30.769 0.00 0.00 0.00 2.40
677 714 6.234920 TCCATTTGAGACGACTTTATTCCAA 58.765 36.000 0.00 0.00 0.00 3.53
698 735 0.035317 ATGTCGCTTCACTGCTTCCA 59.965 50.000 0.00 0.00 0.00 3.53
718 755 1.741706 CCTCGCTGCATCATCTTGTTT 59.258 47.619 0.00 0.00 0.00 2.83
722 759 0.829333 ACTCCTCGCTGCATCATCTT 59.171 50.000 0.00 0.00 0.00 2.40
753 790 1.133915 ACCGTGCACCATTTATAGGGG 60.134 52.381 12.15 4.87 0.00 4.79
828 865 3.057548 CGGATTGCAGCAGCCACA 61.058 61.111 14.68 0.00 41.13 4.17
856 893 1.202770 ACATAGCGTTATCTTGGGGCC 60.203 52.381 0.00 0.00 0.00 5.80
904 941 1.371881 GCCCGAGTATGCTAGCGAC 60.372 63.158 10.77 10.78 0.00 5.19
930 967 4.817063 CCACTCAAATGCGCGGCG 62.817 66.667 19.62 19.62 0.00 6.46
934 971 1.401539 GGTTCTTCCACTCAAATGCGC 60.402 52.381 0.00 0.00 35.97 6.09
1001 1038 6.048732 TCAATAGGATAGCACACAAGTTCA 57.951 37.500 0.00 0.00 0.00 3.18
1035 1072 2.084610 TGTCTTCCTCGCTTGTCATG 57.915 50.000 0.00 0.00 0.00 3.07
1036 1073 2.625737 CATGTCTTCCTCGCTTGTCAT 58.374 47.619 0.00 0.00 0.00 3.06
1041 1078 1.078143 GGCCATGTCTTCCTCGCTT 60.078 57.895 0.00 0.00 0.00 4.68
1042 1079 2.586792 GGCCATGTCTTCCTCGCT 59.413 61.111 0.00 0.00 0.00 4.93
1113 1150 8.800370 TTTCAGCATAGTATTGTGGTAAATGA 57.200 30.769 0.00 0.00 0.00 2.57
1137 1174 7.040409 GGTGGTTTCTTCAGTTTGTCTATCATT 60.040 37.037 0.00 0.00 0.00 2.57
1145 1182 4.340617 TCTTGGTGGTTTCTTCAGTTTGT 58.659 39.130 0.00 0.00 0.00 2.83
1169 1206 7.496529 TTTCTTAGTTCCTCAACATTCAGTG 57.503 36.000 0.00 0.00 34.60 3.66
1178 1230 7.777910 TCAAGTGGAATTTTCTTAGTTCCTCAA 59.222 33.333 5.14 0.00 41.52 3.02
1191 1243 5.930837 TCAACACCTTCAAGTGGAATTTT 57.069 34.783 0.00 0.00 42.28 1.82
1389 1441 6.406692 TCCATACCACTGCTCTCTATTAAC 57.593 41.667 0.00 0.00 0.00 2.01
1556 1611 4.278170 TGTGAGTCAATTGGTTAAAGCAGG 59.722 41.667 5.42 0.00 0.00 4.85
1639 1694 1.908340 CTTGTGGGCTGAGGAGGGAG 61.908 65.000 0.00 0.00 0.00 4.30
1710 1765 2.977772 ATGAGCTGGAGAGTAAGTGC 57.022 50.000 0.00 0.00 0.00 4.40
1716 1771 9.905713 TTTAATGTAAATTATGAGCTGGAGAGT 57.094 29.630 0.00 0.00 0.00 3.24
1756 1811 5.012239 AGCTTGAGACATAATTGCAGGAAA 58.988 37.500 0.00 0.00 0.00 3.13
1780 1835 1.605753 GGGGTTGTCTTCTTCGCTTT 58.394 50.000 0.00 0.00 0.00 3.51
1932 1987 1.039068 ATGTCTCTCTCCGGCATCAG 58.961 55.000 0.00 0.00 0.00 2.90
2022 2077 5.001232 CCAAATTTCCCGAAGACACTCTTA 58.999 41.667 0.00 0.00 36.73 2.10
2382 2437 2.102252 CCTTCTCCCAGCTCAGTATCAC 59.898 54.545 0.00 0.00 0.00 3.06
2427 2482 0.533755 AGTTATCATGGGCAGCGAGC 60.534 55.000 0.00 0.00 44.65 5.03
2428 2483 1.202568 TCAGTTATCATGGGCAGCGAG 60.203 52.381 0.00 0.00 0.00 5.03
2430 2485 1.802960 GATCAGTTATCATGGGCAGCG 59.197 52.381 0.00 0.00 34.46 5.18
2553 2608 0.608130 TGTCATGTGTCTTCTCCCCG 59.392 55.000 0.00 0.00 0.00 5.73
2555 2610 3.902881 ATCTGTCATGTGTCTTCTCCC 57.097 47.619 0.00 0.00 0.00 4.30
2557 2612 6.200665 GCTATCAATCTGTCATGTGTCTTCTC 59.799 42.308 0.00 0.00 0.00 2.87
2558 2613 6.047870 GCTATCAATCTGTCATGTGTCTTCT 58.952 40.000 0.00 0.00 0.00 2.85
2559 2614 6.047870 AGCTATCAATCTGTCATGTGTCTTC 58.952 40.000 0.00 0.00 0.00 2.87
2560 2615 5.987098 AGCTATCAATCTGTCATGTGTCTT 58.013 37.500 0.00 0.00 0.00 3.01
2561 2616 5.611128 AGCTATCAATCTGTCATGTGTCT 57.389 39.130 0.00 0.00 0.00 3.41
2562 2617 5.236047 GGAAGCTATCAATCTGTCATGTGTC 59.764 44.000 0.00 0.00 0.00 3.67
2563 2618 5.121811 GGAAGCTATCAATCTGTCATGTGT 58.878 41.667 0.00 0.00 0.00 3.72
2564 2619 4.210746 CGGAAGCTATCAATCTGTCATGTG 59.789 45.833 0.00 0.00 0.00 3.21
2565 2620 4.375272 CGGAAGCTATCAATCTGTCATGT 58.625 43.478 0.00 0.00 0.00 3.21
2566 2621 3.744942 CCGGAAGCTATCAATCTGTCATG 59.255 47.826 0.00 0.00 0.00 3.07
2567 2622 3.643320 TCCGGAAGCTATCAATCTGTCAT 59.357 43.478 0.00 0.00 0.00 3.06
2568 2623 3.031013 TCCGGAAGCTATCAATCTGTCA 58.969 45.455 0.00 0.00 0.00 3.58
2569 2624 3.735237 TCCGGAAGCTATCAATCTGTC 57.265 47.619 0.00 0.00 0.00 3.51
2627 2682 3.949754 CCTAGCATTTTCTGAGGCAATCA 59.050 43.478 0.00 0.00 36.21 2.57
2762 2817 4.115516 CACACTATCCTCTCATCCAAACG 58.884 47.826 0.00 0.00 0.00 3.60
2952 3007 0.606604 CACTGCCTGTTACCTACCGT 59.393 55.000 0.00 0.00 0.00 4.83


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

AutoCloner maintained by Alex Coulton.