Multiple sequence alignment - TraesCS2D01G388500

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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 TraesCS2D01G388500 chr2D 100.000 1471 0 0 1665 3135 494650063 494651533 0.000000e+00 2717.0
1 TraesCS2D01G388500 chr2D 100.000 1126 0 0 1 1126 494648399 494649524 0.000000e+00 2080.0
2 TraesCS2D01G388500 chr2A 95.551 1461 42 9 1683 3135 639062499 639061054 0.000000e+00 2316.0
3 TraesCS2D01G388500 chr2A 86.562 893 44 29 182 1041 639063662 639062813 0.000000e+00 915.0
4 TraesCS2D01G388500 chr2A 95.000 60 1 1 2463 2520 73540724 73540665 3.330000e-15 93.5
5 TraesCS2D01G388500 chr2A 91.803 61 2 3 2463 2520 173784972 173785032 7.210000e-12 82.4
6 TraesCS2D01G388500 chr2B 88.477 972 54 21 11 970 582305262 582306187 0.000000e+00 1122.0
7 TraesCS2D01G388500 chr2B 97.227 577 16 0 1667 2243 582306639 582307215 0.000000e+00 977.0
8 TraesCS2D01G388500 chr2B 85.744 484 48 6 2654 3135 582307485 582307949 2.810000e-135 492.0
9 TraesCS2D01G388500 chr2B 90.308 227 17 5 2240 2464 715958205 715957982 3.060000e-75 292.0
10 TraesCS2D01G388500 chr2B 89.427 227 19 5 2240 2464 715946414 715946191 6.620000e-72 281.0
11 TraesCS2D01G388500 chr2B 92.818 181 13 0 2284 2464 582307216 582307396 2.400000e-66 263.0
12 TraesCS2D01G388500 chr2B 97.778 45 1 0 2848 2892 715958334 715958290 9.320000e-11 78.7
13 TraesCS2D01G388500 chr2B 90.164 61 3 3 2463 2520 222090189 222090249 3.350000e-10 76.8
14 TraesCS2D01G388500 chr2B 90.164 61 3 3 2463 2520 222094814 222094874 3.350000e-10 76.8
15 TraesCS2D01G388500 chr2B 97.619 42 1 0 2851 2892 715946540 715946499 4.340000e-09 73.1
16 TraesCS2D01G388500 chr6B 90.367 218 19 2 2240 2457 619717440 619717225 5.120000e-73 285.0
17 TraesCS2D01G388500 chr6B 100.000 43 0 0 2848 2890 619717569 619717527 2.590000e-11 80.5
18 TraesCS2D01G388500 chr6B 93.750 48 3 0 2524 2571 619717219 619717172 4.340000e-09 73.1
19 TraesCS2D01G388500 chr5B 88.991 218 22 2 2240 2457 71796112 71796327 5.150000e-68 268.0
20 TraesCS2D01G388500 chr5B 95.556 45 2 0 2848 2892 71795983 71796027 4.340000e-09 73.1
21 TraesCS2D01G388500 chr1A 88.991 218 22 2 2240 2457 77095982 77096197 5.150000e-68 268.0
22 TraesCS2D01G388500 chr1A 95.556 45 2 0 2848 2892 77095853 77095897 4.340000e-09 73.1
23 TraesCS2D01G388500 chr3B 88.532 218 24 1 2240 2457 41834431 41834215 2.400000e-66 263.0
24 TraesCS2D01G388500 chr7D 93.651 63 4 0 2463 2525 111055310 111055248 9.260000e-16 95.3
25 TraesCS2D01G388500 chr4D 89.552 67 6 1 2455 2520 40796813 40796879 2.000000e-12 84.2
26 TraesCS2D01G388500 chr4B 88.710 62 1 3 2463 2518 35022479 35022540 1.560000e-08 71.3
27 TraesCS2D01G388500 chr5A 85.714 63 8 1 2455 2517 269770975 269771036 7.260000e-07 65.8


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 TraesCS2D01G388500 chr2D 494648399 494651533 3134 False 2398.5 2717 100.0000 1 3135 2 chr2D.!!$F1 3134
1 TraesCS2D01G388500 chr2A 639061054 639063662 2608 True 1615.5 2316 91.0565 182 3135 2 chr2A.!!$R2 2953
2 TraesCS2D01G388500 chr2B 582305262 582307949 2687 False 713.5 1122 91.0665 11 3135 4 chr2B.!!$F3 3124

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
441 448 0.029834 GTCGCATCCCATTCACATGC 59.970 55.0 0.0 0.0 39.70 4.06 F
676 700 0.032678 CGCACTCCTCTCGCCAATAT 59.967 55.0 0.0 0.0 0.00 1.28 F
738 762 0.606401 TCCAGCTTTTCCTTCCAGCG 60.606 55.0 0.0 0.0 38.66 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1903 1941 1.679898 CCGCTTCCTCTTCTTGGGT 59.320 57.895 0.00 0.0 0.00 4.51 R
2085 2126 4.035102 GGCCTTCCAGGAGCCGTT 62.035 66.667 3.96 0.0 37.67 4.44 R
2688 2730 1.139163 TCGTTTTTAAGACGTCCCGC 58.861 50.000 13.01 0.0 41.08 6.13 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
109 110 3.488090 GCCTCGCACGCTACCAAC 61.488 66.667 0.00 0.00 0.00 3.77
119 120 3.475774 CTACCAACCGCACGACGC 61.476 66.667 0.00 0.00 41.76 5.19
127 128 2.127270 CGCACGACGCAGCATTTT 60.127 55.556 12.49 0.00 42.60 1.82
128 129 1.725625 CGCACGACGCAGCATTTTT 60.726 52.632 12.49 0.00 42.60 1.94
129 130 1.655697 CGCACGACGCAGCATTTTTC 61.656 55.000 12.49 0.00 42.60 2.29
130 131 1.655697 GCACGACGCAGCATTTTTCG 61.656 55.000 7.87 0.00 41.79 3.46
313 316 4.988598 CCGGACCAGCGCAACTGT 62.989 66.667 11.47 0.00 45.68 3.55
314 317 2.972505 CGGACCAGCGCAACTGTT 60.973 61.111 11.47 0.00 45.68 3.16
433 440 4.241555 GGCCTCGTCGCATCCCAT 62.242 66.667 0.00 0.00 0.00 4.00
434 441 2.203070 GCCTCGTCGCATCCCATT 60.203 61.111 0.00 0.00 0.00 3.16
438 445 0.460109 CTCGTCGCATCCCATTCACA 60.460 55.000 0.00 0.00 0.00 3.58
439 446 0.177836 TCGTCGCATCCCATTCACAT 59.822 50.000 0.00 0.00 0.00 3.21
441 448 0.029834 GTCGCATCCCATTCACATGC 59.970 55.000 0.00 0.00 39.70 4.06
460 469 4.819761 GCCATGCGACGCTCCTCA 62.820 66.667 22.08 0.00 0.00 3.86
463 472 1.227060 CATGCGACGCTCCTCATCA 60.227 57.895 22.08 0.00 0.00 3.07
467 476 1.803289 CGACGCTCCTCATCACTCA 59.197 57.895 0.00 0.00 0.00 3.41
471 480 1.607801 CGCTCCTCATCACTCACCCA 61.608 60.000 0.00 0.00 0.00 4.51
676 700 0.032678 CGCACTCCTCTCGCCAATAT 59.967 55.000 0.00 0.00 0.00 1.28
677 701 1.539065 CGCACTCCTCTCGCCAATATT 60.539 52.381 0.00 0.00 0.00 1.28
679 703 3.615110 CGCACTCCTCTCGCCAATATTAT 60.615 47.826 0.00 0.00 0.00 1.28
681 705 4.153117 GCACTCCTCTCGCCAATATTATTG 59.847 45.833 9.09 9.09 0.00 1.90
684 708 4.894784 TCCTCTCGCCAATATTATTGTCC 58.105 43.478 13.87 5.35 0.00 4.02
738 762 0.606401 TCCAGCTTTTCCTTCCAGCG 60.606 55.000 0.00 0.00 38.66 5.18
742 766 1.790387 CTTTTCCTTCCAGCGCTCG 59.210 57.895 7.13 0.00 0.00 5.03
743 767 1.639298 CTTTTCCTTCCAGCGCTCGG 61.639 60.000 7.13 13.56 0.00 4.63
744 768 4.760047 TTCCTTCCAGCGCTCGGC 62.760 66.667 7.13 0.00 44.05 5.54
920 953 4.162690 CACCTCCTGTAGCCGCCC 62.163 72.222 0.00 0.00 0.00 6.13
1069 1107 4.779733 GCTGGACCCCCGAGGAGA 62.780 72.222 0.00 0.00 39.89 3.71
1070 1108 2.760385 CTGGACCCCCGAGGAGAC 60.760 72.222 0.00 0.00 39.89 3.36
1071 1109 4.393778 TGGACCCCCGAGGAGACC 62.394 72.222 0.00 0.00 39.89 3.85
1073 1111 4.755507 GACCCCCGAGGAGACCGT 62.756 72.222 0.00 0.00 39.89 4.83
1074 1112 4.755507 ACCCCCGAGGAGACCGTC 62.756 72.222 0.00 0.00 39.89 4.79
1080 1118 4.539881 GAGGAGACCGTCGCGCTC 62.540 72.222 5.56 0.88 0.00 5.03
1843 1881 3.459063 CCTTCGTCGTCCCCCTCC 61.459 72.222 0.00 0.00 0.00 4.30
2255 2297 6.844388 TCCTTCATATACTCCATGTACCTGTT 59.156 38.462 0.00 0.00 33.45 3.16
2471 2513 9.138596 GTGAGGAAGATATAATATACTCCCTCC 57.861 40.741 0.00 6.56 36.53 4.30
2486 2528 4.102681 ACTCCCTCCGTCCCATAATTTAAG 59.897 45.833 0.00 0.00 0.00 1.85
2730 2772 6.625532 ATGGTCCCAGCTTGATTTAATTTT 57.374 33.333 0.00 0.00 0.00 1.82
2795 2837 1.982958 TCCTGAACCCTAGTTTCCCAC 59.017 52.381 0.00 0.00 35.94 4.61
2814 2856 1.489824 CGTTGGGCTTTACGTCACG 59.510 57.895 0.00 0.00 33.33 4.35
2834 2877 2.716217 GGCTGGCTGATTTAGTGAACT 58.284 47.619 0.00 0.00 0.00 3.01
2840 2883 5.616270 TGGCTGATTTAGTGAACTTACACA 58.384 37.500 0.00 0.00 42.45 3.72
2893 2936 6.461640 TGGCCTCACTTTTAGTAACTCTAAC 58.538 40.000 3.32 0.00 38.22 2.34
2928 2971 3.070748 GGTTTGTTGCTGTGTGGTTTTT 58.929 40.909 0.00 0.00 0.00 1.94
2948 2991 8.647226 GGTTTTTAATTTGCAGCATAGTTAGTG 58.353 33.333 0.00 0.00 0.00 2.74
2981 3024 6.351286 GGCCATTGAAAAATTGAGTATCCTGT 60.351 38.462 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
431 438 1.590525 GCATGGCCGCATGTGAATG 60.591 57.895 8.11 9.61 35.16 2.67
432 439 2.809706 GCATGGCCGCATGTGAAT 59.190 55.556 8.11 0.00 35.16 2.57
433 440 3.813143 CGCATGGCCGCATGTGAA 61.813 61.111 8.11 0.00 43.56 3.18
434 441 4.774503 TCGCATGGCCGCATGTGA 62.775 61.111 13.75 13.75 46.11 3.58
452 461 1.142748 GGGTGAGTGATGAGGAGCG 59.857 63.158 0.00 0.00 0.00 5.03
455 464 1.267574 GGCTGGGTGAGTGATGAGGA 61.268 60.000 0.00 0.00 0.00 3.71
457 466 1.222936 GGGCTGGGTGAGTGATGAG 59.777 63.158 0.00 0.00 0.00 2.90
460 469 3.402681 CCGGGCTGGGTGAGTGAT 61.403 66.667 3.77 0.00 0.00 3.06
463 472 4.954118 TGACCGGGCTGGGTGAGT 62.954 66.667 18.49 0.00 44.64 3.41
699 723 6.294176 GCTGGATGCTCGTGGAAATTATAATT 60.294 38.462 4.81 4.81 38.95 1.40
700 724 5.182001 GCTGGATGCTCGTGGAAATTATAAT 59.818 40.000 0.00 0.00 38.95 1.28
701 725 4.515191 GCTGGATGCTCGTGGAAATTATAA 59.485 41.667 0.00 0.00 38.95 0.98
702 726 4.065088 GCTGGATGCTCGTGGAAATTATA 58.935 43.478 0.00 0.00 38.95 0.98
703 727 2.880890 GCTGGATGCTCGTGGAAATTAT 59.119 45.455 0.00 0.00 38.95 1.28
751 775 4.292178 GAGCGGATCGGAGGGCTG 62.292 72.222 4.16 0.00 35.54 4.85
907 940 1.847798 ATGTTTGGGCGGCTACAGGA 61.848 55.000 9.56 0.00 0.00 3.86
909 942 0.676466 TCATGTTTGGGCGGCTACAG 60.676 55.000 9.56 5.91 0.00 2.74
920 953 1.361668 CGGAGGCGGAGTCATGTTTG 61.362 60.000 0.00 0.00 0.00 2.93
1052 1090 4.779733 TCTCCTCGGGGGTCCAGC 62.780 72.222 0.00 0.00 36.25 4.85
1053 1091 2.760385 GTCTCCTCGGGGGTCCAG 60.760 72.222 0.00 0.00 36.25 3.86
1054 1092 4.393778 GGTCTCCTCGGGGGTCCA 62.394 72.222 0.00 0.00 36.25 4.02
1056 1094 4.755507 ACGGTCTCCTCGGGGGTC 62.756 72.222 0.00 0.00 36.25 4.46
1057 1095 4.755507 GACGGTCTCCTCGGGGGT 62.756 72.222 0.00 0.00 36.25 4.95
1903 1941 1.679898 CCGCTTCCTCTTCTTGGGT 59.320 57.895 0.00 0.00 0.00 4.51
2085 2126 4.035102 GGCCTTCCAGGAGCCGTT 62.035 66.667 3.96 0.00 37.67 4.44
2255 2297 4.413189 ACAACCATGATCCATCAGACCATA 59.587 41.667 0.00 0.00 40.64 2.74
2471 2513 4.630894 TGCAAGCTTAAATTATGGGACG 57.369 40.909 0.00 0.00 0.00 4.79
2486 2528 7.538678 CCCATAATATAAGATCGTTTTGCAAGC 59.461 37.037 0.00 0.00 0.00 4.01
2688 2730 1.139163 TCGTTTTTAAGACGTCCCGC 58.861 50.000 13.01 0.00 41.08 6.13
2795 2837 1.864176 GTGACGTAAAGCCCAACGG 59.136 57.895 7.17 0.00 43.25 4.44
2814 2856 2.716217 AGTTCACTAAATCAGCCAGCC 58.284 47.619 0.00 0.00 0.00 4.85
2840 2883 3.571401 GGAGCAAGCATAGGCACAATAAT 59.429 43.478 0.67 0.00 44.61 1.28
2928 2971 4.887071 CCCCACTAACTATGCTGCAAATTA 59.113 41.667 6.36 5.02 0.00 1.40
2981 3024 5.224441 ACCACCCAGATAGAAATAAGGCTA 58.776 41.667 0.00 0.00 0.00 3.93
3075 3118 4.835284 TGGTTCCATACTGCTATGAACA 57.165 40.909 0.00 0.00 32.66 3.18
3079 3122 4.422073 TCCTTGGTTCCATACTGCTATG 57.578 45.455 0.00 0.00 0.00 2.23
3110 3156 0.249489 GTAGATACAGGGTGCTGCCG 60.249 60.000 0.00 0.00 38.44 5.69


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

AutoCloner maintained by Alex Coulton.