Multiple sequence alignment - TraesCS1A01G178600

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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 TraesCS1A01G178600 chr1A 100.000 3128 0 0 1 3128 323193726 323190599 0.000000e+00 5777
1 TraesCS1A01G178600 chr1A 90.978 787 44 7 7 778 219987753 219986979 0.000000e+00 1035
2 TraesCS1A01G178600 chr1D 93.866 2315 94 18 832 3128 252477389 252479673 0.000000e+00 3445
3 TraesCS1A01G178600 chr1D 81.928 166 27 3 215 379 463984400 463984563 1.510000e-28 137
4 TraesCS1A01G178600 chr1B 95.433 2146 93 3 777 2920 361016604 361014462 0.000000e+00 3415
5 TraesCS1A01G178600 chr1B 88.444 225 8 4 2914 3128 361014303 361014087 4.000000e-64 255
6 TraesCS1A01G178600 chr7D 84.395 801 84 15 1 790 267752687 267751917 0.000000e+00 749
7 TraesCS1A01G178600 chr3B 83.523 789 100 15 1 780 830679252 830680019 0.000000e+00 710
8 TraesCS1A01G178600 chr3B 83.270 789 102 16 1 780 830391876 830392643 0.000000e+00 699
9 TraesCS1A01G178600 chr3B 82.838 740 112 9 47 777 803518090 803517357 0.000000e+00 649
10 TraesCS1A01G178600 chr6D 83.228 793 98 16 1 780 327619972 327619202 0.000000e+00 695
11 TraesCS1A01G178600 chr6D 85.577 104 13 2 777 878 9536190 9536293 1.190000e-19 108
12 TraesCS1A01G178600 chr5A 82.614 788 107 13 1 778 561556341 561555574 0.000000e+00 669
13 TraesCS1A01G178600 chr5A 81.517 633 103 11 151 778 340978471 340979094 2.780000e-140 508
14 TraesCS1A01G178600 chr4D 81.546 634 105 11 151 778 323150300 323149673 2.150000e-141 512
15 TraesCS1A01G178600 chr7B 83.918 485 59 12 292 769 585721360 585720888 2.210000e-121 446
16 TraesCS1A01G178600 chr6A 84.228 298 36 7 200 495 524289545 524289257 2.380000e-71 279


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 TraesCS1A01G178600 chr1A 323190599 323193726 3127 True 5777 5777 100.0000 1 3128 1 chr1A.!!$R2 3127
1 TraesCS1A01G178600 chr1A 219986979 219987753 774 True 1035 1035 90.9780 7 778 1 chr1A.!!$R1 771
2 TraesCS1A01G178600 chr1D 252477389 252479673 2284 False 3445 3445 93.8660 832 3128 1 chr1D.!!$F1 2296
3 TraesCS1A01G178600 chr1B 361014087 361016604 2517 True 1835 3415 91.9385 777 3128 2 chr1B.!!$R1 2351
4 TraesCS1A01G178600 chr7D 267751917 267752687 770 True 749 749 84.3950 1 790 1 chr7D.!!$R1 789
5 TraesCS1A01G178600 chr3B 830679252 830680019 767 False 710 710 83.5230 1 780 1 chr3B.!!$F2 779
6 TraesCS1A01G178600 chr3B 830391876 830392643 767 False 699 699 83.2700 1 780 1 chr3B.!!$F1 779
7 TraesCS1A01G178600 chr3B 803517357 803518090 733 True 649 649 82.8380 47 777 1 chr3B.!!$R1 730
8 TraesCS1A01G178600 chr6D 327619202 327619972 770 True 695 695 83.2280 1 780 1 chr6D.!!$R1 779
9 TraesCS1A01G178600 chr5A 561555574 561556341 767 True 669 669 82.6140 1 778 1 chr5A.!!$R1 777
10 TraesCS1A01G178600 chr5A 340978471 340979094 623 False 508 508 81.5170 151 778 1 chr5A.!!$F1 627
11 TraesCS1A01G178600 chr4D 323149673 323150300 627 True 512 512 81.5460 151 778 1 chr4D.!!$R1 627

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
196 212 0.036765 TAGTGCAGGCCGTGGTTTAG 60.037 55.0 0.00 0.0 0.00 1.85 F
1578 1621 0.529992 CTCCGGCGGTGGATAAGAAC 60.530 60.0 27.32 0.0 37.41 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1617 1660 0.478507 CCTTGGTCAACCTGAACCCT 59.521 55.0 0.1 0.0 31.76 4.34 R
3016 3225 0.622665 AGCTAGATGCACCAGGCTTT 59.377 50.0 0.0 0.0 45.94 3.51 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
34 35 2.076863 CATGTTCCTCTCGTGGTTTCC 58.923 52.381 0.00 0.00 0.00 3.13
73 74 3.233507 ACATCCACAAAACATGCTCCTT 58.766 40.909 0.00 0.00 0.00 3.36
96 97 0.735978 CCGCGCTAGTCATGTGTGAA 60.736 55.000 5.56 0.00 35.80 3.18
124 125 0.894184 GGATCGATCGTGGAGGCCTA 60.894 60.000 18.81 0.00 0.00 3.93
135 136 1.315216 GAGGCCTAGAGGGTTCCCT 59.685 63.158 4.42 10.51 39.51 4.20
196 212 0.036765 TAGTGCAGGCCGTGGTTTAG 60.037 55.000 0.00 0.00 0.00 1.85
205 221 2.227149 GGCCGTGGTTTAGGTGTTTAAG 59.773 50.000 0.00 0.00 0.00 1.85
234 250 1.216710 GTCTGCCGCTAGCTTGTCT 59.783 57.895 13.93 0.00 44.23 3.41
262 278 7.202047 CCTGATTAACTTTGGCTCCTAGAGTAT 60.202 40.741 0.00 0.00 31.39 2.12
341 360 2.905075 TCGGTACTTGCCTCATTGATG 58.095 47.619 0.00 0.00 0.00 3.07
385 404 2.174360 TCAGGACAGGACATGAGACTG 58.826 52.381 0.00 7.10 38.19 3.51
412 431 7.763071 GGTTAGTTAGACGGTTCATCTAATTGT 59.237 37.037 0.00 0.00 40.03 2.71
457 479 2.837532 TGTTATGTGCTGACTGCTGA 57.162 45.000 5.87 0.00 43.37 4.26
464 490 1.857217 GTGCTGACTGCTGATGTATCG 59.143 52.381 5.87 0.00 43.37 2.92
561 588 9.029368 AGAAGATTGATTACGAGGATATCATGA 57.971 33.333 4.83 0.00 0.00 3.07
566 593 8.818141 TTGATTACGAGGATATCATGAAAGAC 57.182 34.615 0.00 0.00 0.00 3.01
800 838 2.410785 CAATGTATTGCGCAGATGGG 57.589 50.000 11.31 0.00 0.00 4.00
805 843 3.814625 TGTATTGCGCAGATGGGAAATA 58.185 40.909 11.31 6.28 37.42 1.40
807 845 5.555966 TGTATTGCGCAGATGGGAAATATA 58.444 37.500 11.31 7.91 39.64 0.86
911 954 0.674895 CGAAGCCCTTGGTTGGAGAG 60.675 60.000 0.00 0.00 30.25 3.20
1398 1441 3.680920 ATCCCGCTCCGTCCCTCTT 62.681 63.158 0.00 0.00 0.00 2.85
1401 1444 4.856607 CGCTCCGTCCCTCTTCGC 62.857 72.222 0.00 0.00 0.00 4.70
1497 1540 2.286121 TTCCGCCTCTCCCCCAAT 60.286 61.111 0.00 0.00 0.00 3.16
1530 1573 2.538512 GAACCCACGTTCTACACCTT 57.461 50.000 0.00 0.00 44.29 3.50
1543 1586 3.066190 ACCTTGTCGCGGATCCGA 61.066 61.111 37.64 15.51 42.83 4.55
1550 1593 4.925576 CGCGGATCCGACGAAGGG 62.926 72.222 37.64 11.47 42.83 3.95
1554 1597 1.837499 GGATCCGACGAAGGGGGAT 60.837 63.158 0.00 0.00 44.40 3.85
1578 1621 0.529992 CTCCGGCGGTGGATAAGAAC 60.530 60.000 27.32 0.00 37.41 3.01
1641 1684 3.400255 GTTCAGGTTGACCAAGGAGTAC 58.600 50.000 2.56 0.00 38.89 2.73
1701 1744 1.012841 GACCGTACGAGGTAGTGGAG 58.987 60.000 18.76 0.00 46.09 3.86
1706 1749 1.671845 GTACGAGGTAGTGGAGCAGAG 59.328 57.143 0.00 0.00 0.00 3.35
1708 1751 0.394488 CGAGGTAGTGGAGCAGAGGA 60.394 60.000 0.00 0.00 0.00 3.71
1839 1882 2.036089 GGAGAAGTTCAGTCAGTTCCGT 59.964 50.000 5.50 0.00 0.00 4.69
2072 2115 6.647334 TTCTAATGCCAACATGTCTTCAAA 57.353 33.333 0.00 0.00 36.36 2.69
2075 2118 3.663995 TGCCAACATGTCTTCAAATGG 57.336 42.857 0.00 2.01 0.00 3.16
2192 2235 5.769662 GGAGGTTGTGCAATTCATGGATATA 59.230 40.000 0.00 0.00 0.00 0.86
2238 2281 0.104120 GTGTTTGGCCCAACTTGGAC 59.896 55.000 19.58 6.69 40.96 4.02
2240 2283 1.830408 TTTGGCCCAACTTGGACGG 60.830 57.895 9.61 0.00 40.96 4.79
2241 2284 4.966787 TGGCCCAACTTGGACGGC 62.967 66.667 9.61 6.54 40.96 5.68
2245 2288 3.055719 CCAACTTGGACGGCGCAT 61.056 61.111 10.83 0.00 40.96 4.73
2249 2292 1.937223 CAACTTGGACGGCGCATATAA 59.063 47.619 10.83 0.00 0.00 0.98
2304 2348 3.019564 GGATGTTTCTTCAGGGATGGTG 58.980 50.000 0.00 0.00 0.00 4.17
2317 2361 1.410153 GGATGGTGGTCAATTGGCATC 59.590 52.381 12.93 5.99 0.00 3.91
2352 2396 7.764443 GCCAGTATACTCAAAACTCAGATTACA 59.236 37.037 1.26 0.00 0.00 2.41
2499 2543 4.329462 AGGTCAAGACTCAAGACTGAAC 57.671 45.455 0.00 0.00 32.98 3.18
2585 2629 4.144051 GTGTTGCTTATTGTTGTTTCGTCG 59.856 41.667 0.00 0.00 0.00 5.12
2589 2633 3.117346 GCTTATTGTTGTTTCGTCGTTGC 59.883 43.478 0.00 0.00 0.00 4.17
2655 2699 7.876582 ACCTAGACCAACAACTACAGTTAATTC 59.123 37.037 0.00 0.00 36.32 2.17
2759 2803 3.317603 TGCTTATTTGGGCTTTTCTGC 57.682 42.857 0.00 0.00 0.00 4.26
2910 2954 2.412870 TGCATGTAGTTGGACGTCTTG 58.587 47.619 16.46 0.00 0.00 3.02
2970 3179 6.319399 TCATAGTTGGCACGTATGATATACG 58.681 40.000 17.01 17.01 45.44 3.06
2971 3180 3.909430 AGTTGGCACGTATGATATACGG 58.091 45.455 21.05 13.03 44.38 4.02
2972 3181 3.570975 AGTTGGCACGTATGATATACGGA 59.429 43.478 21.05 4.25 44.38 4.69
2973 3182 3.842732 TGGCACGTATGATATACGGAG 57.157 47.619 21.05 15.17 44.38 4.63
3003 3212 6.216569 TCAAGTGCTCCGATAGAATATTCAC 58.783 40.000 17.56 7.55 39.76 3.18
3120 3339 5.705609 ACACGAAAAAGTCCTTGCATATT 57.294 34.783 0.00 0.00 0.00 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 1.087771 GTACCTGTTTCGGCGATGGG 61.088 60.000 11.76 12.92 0.00 4.00
43 44 5.508200 TGTTTTGTGGATGTACCTGTTTC 57.492 39.130 0.00 0.00 39.86 2.78
73 74 1.375396 ACATGACTAGCGCGGCAAA 60.375 52.632 8.83 0.00 0.00 3.68
96 97 2.034685 CCACGATCGATCCTACACATGT 59.965 50.000 24.34 6.19 0.00 3.21
178 193 1.302511 CTAAACCACGGCCTGCACT 60.303 57.895 0.00 0.00 0.00 4.40
188 203 6.426025 CAGGAGTACTTAAACACCTAAACCAC 59.574 42.308 0.00 0.00 38.25 4.16
190 205 5.410746 GCAGGAGTACTTAAACACCTAAACC 59.589 44.000 0.00 0.00 38.25 3.27
196 212 2.289257 ACGGCAGGAGTACTTAAACACC 60.289 50.000 0.00 0.00 0.00 4.16
234 250 4.657814 AGGAGCCAAAGTTAATCAGGAA 57.342 40.909 0.00 0.00 0.00 3.36
367 386 1.566211 CCAGTCTCATGTCCTGTCCT 58.434 55.000 0.00 0.00 0.00 3.85
385 404 4.732672 AGATGAACCGTCTAACTAACCC 57.267 45.455 0.00 0.00 0.00 4.11
412 431 7.757941 TTGGAGATTATGTGTCAATGTTTGA 57.242 32.000 0.00 0.00 37.33 2.69
424 446 7.557358 TCAGCACATAACAATTGGAGATTATGT 59.443 33.333 19.05 19.05 44.94 2.29
525 552 8.879427 TCGTAATCAATCTTCTCCCTATGATA 57.121 34.615 0.00 0.00 0.00 2.15
805 843 9.942850 AAAAATTCAAACGATTCCTGGAATTAT 57.057 25.926 22.15 11.28 34.81 1.28
807 845 7.307930 GCAAAAATTCAAACGATTCCTGGAATT 60.308 33.333 22.15 5.61 36.75 2.17
819 857 6.879962 AGATGAATGTGCAAAAATTCAAACG 58.120 32.000 19.01 0.00 43.86 3.60
827 865 5.787953 TTCTGGAGATGAATGTGCAAAAA 57.212 34.783 0.00 0.00 0.00 1.94
911 954 1.353103 CAAATGGATGCGGCGTCTC 59.647 57.895 20.61 11.88 0.00 3.36
1224 1267 0.543174 AGAGGCGGAGAAAGTGGAGT 60.543 55.000 0.00 0.00 0.00 3.85
1530 1573 3.391160 CTTCGTCGGATCCGCGACA 62.391 63.158 36.12 27.89 43.20 4.35
1543 1586 0.618981 GGAGTGAAATCCCCCTTCGT 59.381 55.000 0.00 0.00 32.79 3.85
1550 1593 2.513897 CCGCCGGAGTGAAATCCC 60.514 66.667 5.05 0.00 35.82 3.85
1554 1597 1.259142 TATCCACCGCCGGAGTGAAA 61.259 55.000 22.64 12.66 38.83 2.69
1578 1621 4.867599 GCGTACTTCTCCGGCCGG 62.868 72.222 39.13 39.13 0.00 6.13
1617 1660 0.478507 CCTTGGTCAACCTGAACCCT 59.521 55.000 0.10 0.00 31.76 4.34
1627 1670 1.621814 CTTCCGGTACTCCTTGGTCAA 59.378 52.381 0.00 0.00 0.00 3.18
1641 1684 0.977395 ACTCCTTCACCTTCTTCCGG 59.023 55.000 0.00 0.00 0.00 5.14
1683 1726 1.028868 GCTCCACTACCTCGTACGGT 61.029 60.000 16.52 8.94 41.10 4.83
1701 1744 3.267860 CTCGCGCCAATCCTCTGC 61.268 66.667 0.00 0.00 0.00 4.26
1706 1749 2.817423 CTCTTGCTCGCGCCAATCC 61.817 63.158 0.00 0.00 34.43 3.01
1708 1751 2.821366 CCTCTTGCTCGCGCCAAT 60.821 61.111 0.00 0.00 34.43 3.16
1725 1768 0.959553 TCCTCGCCATCTTCGATACC 59.040 55.000 0.00 0.00 35.25 2.73
1839 1882 1.619827 ACGTCGATCCCAAACCACTTA 59.380 47.619 0.00 0.00 0.00 2.24
2075 2118 2.432972 CTTTGGCACCGGCATTGC 60.433 61.111 0.00 3.60 43.71 3.56
2084 2127 0.723981 GTCATCGCTCTCTTTGGCAC 59.276 55.000 0.00 0.00 0.00 5.01
2165 2208 3.367703 CCATGAATTGCACAACCTCCTTC 60.368 47.826 0.00 0.00 0.00 3.46
2192 2235 5.049886 GCTTAACAGGTTACGCTAAACAAGT 60.050 40.000 11.92 0.00 37.34 3.16
2238 2281 2.475111 CACCACTAACTTATATGCGCCG 59.525 50.000 4.18 0.00 0.00 6.46
2240 2283 2.869801 TGCACCACTAACTTATATGCGC 59.130 45.455 0.00 0.00 34.32 6.09
2241 2284 4.368315 TCTGCACCACTAACTTATATGCG 58.632 43.478 0.00 0.00 34.32 4.73
2245 2288 6.747414 ATGGATCTGCACCACTAACTTATA 57.253 37.500 0.00 0.00 40.36 0.98
2249 2292 4.655649 TCATATGGATCTGCACCACTAACT 59.344 41.667 2.13 0.00 40.36 2.24
2317 2361 7.875041 AGTTTTGAGTATACTGGCTAGCATATG 59.125 37.037 18.24 0.00 0.00 1.78
2499 2543 2.839486 TCAACCAAGTGCTACTGAGG 57.161 50.000 0.00 0.00 32.38 3.86
2552 2596 4.278419 ACAATAAGCAACACCAAGGAACTC 59.722 41.667 0.00 0.00 38.49 3.01
2585 2629 2.223340 CCTTCATTAGGCATGTCGCAAC 60.223 50.000 0.00 0.00 45.17 4.17
2589 2633 2.158900 AGGTCCTTCATTAGGCATGTCG 60.159 50.000 0.00 0.00 44.37 4.35
2655 2699 8.970859 AAGAATAATCTGGTGGATAAACTGAG 57.029 34.615 0.00 0.00 35.59 3.35
2759 2803 9.981114 AAACTAGGAAAAACATAAAGTGGATTG 57.019 29.630 0.00 0.00 0.00 2.67
2799 2843 6.599638 GTGCCTATCAACTTAATCAGGACTTT 59.400 38.462 0.00 0.00 0.00 2.66
2970 3179 2.094182 TCGGAGCACTTGATTGTACTCC 60.094 50.000 4.33 4.33 43.60 3.85
2971 3180 3.232213 TCGGAGCACTTGATTGTACTC 57.768 47.619 0.00 0.00 31.40 2.59
2972 3181 3.895232 ATCGGAGCACTTGATTGTACT 57.105 42.857 0.00 0.00 0.00 2.73
2973 3182 4.933330 TCTATCGGAGCACTTGATTGTAC 58.067 43.478 0.00 0.00 0.00 2.90
2974 3183 5.592104 TTCTATCGGAGCACTTGATTGTA 57.408 39.130 0.00 0.00 0.00 2.41
2975 3184 4.471904 TTCTATCGGAGCACTTGATTGT 57.528 40.909 0.00 0.00 0.00 2.71
2976 3185 7.386025 TGAATATTCTATCGGAGCACTTGATTG 59.614 37.037 16.24 0.00 0.00 2.67
2977 3186 7.386299 GTGAATATTCTATCGGAGCACTTGATT 59.614 37.037 16.24 0.00 0.00 2.57
2978 3187 6.870965 GTGAATATTCTATCGGAGCACTTGAT 59.129 38.462 16.24 0.00 0.00 2.57
3003 3212 5.294552 GCACCAGGCTTTCTTAGTACAATAG 59.705 44.000 0.00 0.00 40.25 1.73
3016 3225 0.622665 AGCTAGATGCACCAGGCTTT 59.377 50.000 0.00 0.00 45.94 3.51


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

AutoCloner maintained by Alex Coulton.