Multiple sequence alignment - TraesCS2A01G475300

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 TraesCS2A01G475300 chr2A 100.000 4308 0 0 1 4308 715918972 715914665 0.000000e+00 7956.0
1 TraesCS2A01G475300 chr2A 85.151 1394 150 22 960 2329 715951255 715949895 0.000000e+00 1375.0
2 TraesCS2A01G475300 chr2A 87.553 940 89 19 2714 3634 715890501 715891431 0.000000e+00 1062.0
3 TraesCS2A01G475300 chr2A 81.470 1333 196 26 970 2278 716163620 716164925 0.000000e+00 1046.0
4 TraesCS2A01G475300 chr2D 95.725 1965 60 9 689 2648 577535916 577537861 0.000000e+00 3142.0
5 TraesCS2A01G475300 chr2D 96.745 1659 40 7 2654 4308 577537899 577539547 0.000000e+00 2752.0
6 TraesCS2A01G475300 chr2D 84.426 1586 166 34 2714 4266 577579902 577578365 0.000000e+00 1485.0
7 TraesCS2A01G475300 chr2D 85.460 1348 148 17 996 2329 577581911 577580598 0.000000e+00 1360.0
8 TraesCS2A01G475300 chr2D 84.993 1366 160 25 983 2329 577802859 577801520 0.000000e+00 1345.0
9 TraesCS2A01G475300 chr2D 85.282 1189 130 20 1159 2329 577440816 577441977 0.000000e+00 1184.0
10 TraesCS2A01G475300 chr2D 87.558 651 67 11 2722 3367 577442759 577443400 0.000000e+00 741.0
11 TraesCS2A01G475300 chr2D 86.936 643 70 10 2671 3303 577800798 577800160 0.000000e+00 710.0
12 TraesCS2A01G475300 chr2B 94.213 1970 69 14 689 2648 695172403 695170469 0.000000e+00 2964.0
13 TraesCS2A01G475300 chr2B 96.562 1629 44 6 2652 4276 695170433 695168813 0.000000e+00 2687.0
14 TraesCS2A01G475300 chr2B 84.383 1620 185 38 2671 4263 695108949 695110527 0.000000e+00 1528.0
15 TraesCS2A01G475300 chr2B 85.339 1371 140 23 978 2329 695380000 695378672 0.000000e+00 1362.0
16 TraesCS2A01G475300 chr2B 85.251 1356 138 25 996 2326 695106859 695108177 0.000000e+00 1339.0
17 TraesCS2A01G475300 chr2B 82.219 1316 180 25 992 2278 695508136 695509426 0.000000e+00 1085.0
18 TraesCS2A01G475300 chr2B 80.165 1331 212 26 976 2281 695439929 695438626 0.000000e+00 948.0
19 TraesCS2A01G475300 chr2B 87.555 683 41 15 1 677 73310655 73311299 0.000000e+00 750.0
20 TraesCS2A01G475300 chr2B 88.419 639 43 16 46 677 605008450 605009064 0.000000e+00 741.0
21 TraesCS2A01G475300 chr2B 82.979 658 76 16 2674 3319 695437161 695436528 2.910000e-156 562.0
22 TraesCS2A01G475300 chr2B 87.436 390 39 6 2768 3154 695377747 695377365 1.420000e-119 440.0
23 TraesCS2A01G475300 chr6D 93.979 681 27 7 1 677 352980311 352980981 0.000000e+00 1018.0
24 TraesCS2A01G475300 chr6A 91.215 683 40 9 1 681 48684820 48685484 0.000000e+00 911.0
25 TraesCS2A01G475300 chr7A 89.265 680 39 10 1 677 691681599 691682247 0.000000e+00 821.0
26 TraesCS2A01G475300 chr7A 76.699 309 50 15 1 305 78840451 78840741 7.460000e-33 152.0
27 TraesCS2A01G475300 chr7A 88.636 88 5 3 161 245 118474193 118474108 7.620000e-18 102.0
28 TraesCS2A01G475300 chr3D 80.976 205 24 13 110 305 573623877 573623679 9.650000e-32 148.0
29 TraesCS2A01G475300 chr1D 79.730 148 24 3 1 146 492215940 492216083 7.620000e-18 102.0
30 TraesCS2A01G475300 chr7D 86.000 100 6 5 161 257 113592946 113592852 2.740000e-17 100.0
31 TraesCS2A01G475300 chr7B 77.358 159 28 6 1 156 539854740 539854893 2.130000e-13 87.9


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 TraesCS2A01G475300 chr2A 715914665 715918972 4307 True 7956.0 7956 100.0000 1 4308 1 chr2A.!!$R1 4307
1 TraesCS2A01G475300 chr2A 715949895 715951255 1360 True 1375.0 1375 85.1510 960 2329 1 chr2A.!!$R2 1369
2 TraesCS2A01G475300 chr2A 715890501 715891431 930 False 1062.0 1062 87.5530 2714 3634 1 chr2A.!!$F1 920
3 TraesCS2A01G475300 chr2A 716163620 716164925 1305 False 1046.0 1046 81.4700 970 2278 1 chr2A.!!$F2 1308
4 TraesCS2A01G475300 chr2D 577535916 577539547 3631 False 2947.0 3142 96.2350 689 4308 2 chr2D.!!$F2 3619
5 TraesCS2A01G475300 chr2D 577578365 577581911 3546 True 1422.5 1485 84.9430 996 4266 2 chr2D.!!$R1 3270
6 TraesCS2A01G475300 chr2D 577800160 577802859 2699 True 1027.5 1345 85.9645 983 3303 2 chr2D.!!$R2 2320
7 TraesCS2A01G475300 chr2D 577440816 577443400 2584 False 962.5 1184 86.4200 1159 3367 2 chr2D.!!$F1 2208
8 TraesCS2A01G475300 chr2B 695168813 695172403 3590 True 2825.5 2964 95.3875 689 4276 2 chr2B.!!$R1 3587
9 TraesCS2A01G475300 chr2B 695106859 695110527 3668 False 1433.5 1528 84.8170 996 4263 2 chr2B.!!$F4 3267
10 TraesCS2A01G475300 chr2B 695508136 695509426 1290 False 1085.0 1085 82.2190 992 2278 1 chr2B.!!$F3 1286
11 TraesCS2A01G475300 chr2B 695377365 695380000 2635 True 901.0 1362 86.3875 978 3154 2 chr2B.!!$R2 2176
12 TraesCS2A01G475300 chr2B 695436528 695439929 3401 True 755.0 948 81.5720 976 3319 2 chr2B.!!$R3 2343
13 TraesCS2A01G475300 chr2B 73310655 73311299 644 False 750.0 750 87.5550 1 677 1 chr2B.!!$F1 676
14 TraesCS2A01G475300 chr2B 605008450 605009064 614 False 741.0 741 88.4190 46 677 1 chr2B.!!$F2 631
15 TraesCS2A01G475300 chr6D 352980311 352980981 670 False 1018.0 1018 93.9790 1 677 1 chr6D.!!$F1 676
16 TraesCS2A01G475300 chr6A 48684820 48685484 664 False 911.0 911 91.2150 1 681 1 chr6A.!!$F1 680
17 TraesCS2A01G475300 chr7A 691681599 691682247 648 False 821.0 821 89.2650 1 677 1 chr7A.!!$F2 676

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
735 763 0.602562 GCAATACAGGCAGCCAAACA 59.397 50.0 15.8 0.0 0.00 2.83 F
1057 1096 0.757935 TATACCACCCGCTCCCAGTC 60.758 60.0 0.0 0.0 0.00 3.51 F
2043 2127 0.390209 ACTTTGCAATTCGCCCATGC 60.390 50.0 0.0 0.0 41.33 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1711 1795 0.174389 ATGTACTCGCTGACAGCCAG 59.826 55.0 21.55 20.28 45.67 4.85 R
2072 2164 2.039084 GACAAGGACAGGAACCACTCAT 59.961 50.0 0.00 0.00 0.00 2.90 R
3519 5001 0.032540 TCGCTCGCACATAGATGCAT 59.967 50.0 0.00 0.00 46.47 3.96 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
366 384 6.911511 CGTTTGCATTTTTGGAAATTGTTCAT 59.088 30.769 0.00 0.00 33.25 2.57
603 629 7.846066 TCCTCCTTTCAAAAATTCTTCACAAA 58.154 30.769 0.00 0.00 0.00 2.83
605 631 8.768019 CCTCCTTTCAAAAATTCTTCACAAATC 58.232 33.333 0.00 0.00 0.00 2.17
606 632 9.538508 CTCCTTTCAAAAATTCTTCACAAATCT 57.461 29.630 0.00 0.00 0.00 2.40
699 727 8.784043 GTTTACTTTTGTCTCACATGGACTTAT 58.216 33.333 0.00 0.00 35.04 1.73
700 728 8.918202 TTACTTTTGTCTCACATGGACTTATT 57.082 30.769 0.00 0.00 35.04 1.40
735 763 0.602562 GCAATACAGGCAGCCAAACA 59.397 50.000 15.80 0.00 0.00 2.83
766 794 2.285743 GAGCAGGGGAGGAGGGTT 60.286 66.667 0.00 0.00 0.00 4.11
876 905 2.450609 ATCTCGCTAACACAAACCGT 57.549 45.000 0.00 0.00 0.00 4.83
911 940 8.883954 TTATTAATCTCTTCTCTCGTCGACTA 57.116 34.615 14.70 0.95 0.00 2.59
950 980 3.891366 ACCACTTCCATTTCAAAGTCCAG 59.109 43.478 0.00 0.00 33.53 3.86
969 999 1.349357 AGCTCCAAACTCCTCTTCCAC 59.651 52.381 0.00 0.00 0.00 4.02
1055 1094 1.472662 CCTATACCACCCGCTCCCAG 61.473 65.000 0.00 0.00 0.00 4.45
1056 1095 0.759436 CTATACCACCCGCTCCCAGT 60.759 60.000 0.00 0.00 0.00 4.00
1057 1096 0.757935 TATACCACCCGCTCCCAGTC 60.758 60.000 0.00 0.00 0.00 3.51
1152 1197 3.241530 TCTGCCGCCTTCACCTGT 61.242 61.111 0.00 0.00 0.00 4.00
1261 1315 2.744202 CTCTCACACACAATAACTGCCC 59.256 50.000 0.00 0.00 0.00 5.36
1298 1361 1.333636 CCCTCCGCCAGATTCACTCT 61.334 60.000 0.00 0.00 33.14 3.24
1322 1394 1.067846 CCAAGACGATGACACTTCCGA 60.068 52.381 0.00 0.00 0.00 4.55
1323 1395 2.254459 CAAGACGATGACACTTCCGAG 58.746 52.381 0.00 0.00 0.00 4.63
1324 1396 1.535833 AGACGATGACACTTCCGAGT 58.464 50.000 0.00 0.00 36.25 4.18
1520 1604 1.753649 CTCCTGCGAAGAGGATCAGAA 59.246 52.381 0.00 0.00 41.51 3.02
1706 1790 1.378531 TGGCAATGCGAGTCCATTAC 58.621 50.000 0.00 2.61 33.86 1.89
1711 1795 2.588034 GCGAGTCCATTACCGGGC 60.588 66.667 6.32 0.00 0.00 6.13
1974 2058 2.808543 GGATGTCACCAACTGTTCAGTC 59.191 50.000 5.91 0.00 0.00 3.51
2043 2127 0.390209 ACTTTGCAATTCGCCCATGC 60.390 50.000 0.00 0.00 41.33 4.06
2072 2164 1.811965 CGTGCATCAGTTCAAATCCCA 59.188 47.619 0.00 0.00 0.00 4.37
2226 2325 3.264193 AGCCTATTCTTGTGTGACCATGA 59.736 43.478 0.00 0.00 0.00 3.07
2349 2505 3.391955 ACTCGTAGTAGAGGACCTAGCAT 59.608 47.826 0.00 0.00 42.31 3.79
2382 3755 9.784531 TCAACTCTTTGTCTTAATCTCTTGAAT 57.215 29.630 0.00 0.00 34.02 2.57
2511 3886 9.213799 GATGATTACAATTGGATAGAGGAGTTC 57.786 37.037 10.83 0.00 0.00 3.01
2592 3969 7.202056 CCAAAGGTTTCTAATTAGGGGTGTTTT 60.202 37.037 12.54 4.79 0.00 2.43
2593 3970 7.924358 AAGGTTTCTAATTAGGGGTGTTTTT 57.076 32.000 12.54 0.00 0.00 1.94
2648 4025 7.601856 TCCAATTAAACATTCACCACTCATTC 58.398 34.615 0.00 0.00 0.00 2.67
2649 4026 7.451255 TCCAATTAAACATTCACCACTCATTCT 59.549 33.333 0.00 0.00 0.00 2.40
2650 4027 8.739039 CCAATTAAACATTCACCACTCATTCTA 58.261 33.333 0.00 0.00 0.00 2.10
2756 4180 9.139174 ACTTTTTCAATTGCTTTCGTATTATGG 57.861 29.630 0.00 0.00 0.00 2.74
2757 4181 9.139174 CTTTTTCAATTGCTTTCGTATTATGGT 57.861 29.630 0.00 0.00 0.00 3.55
2758 4182 9.482627 TTTTTCAATTGCTTTCGTATTATGGTT 57.517 25.926 0.00 0.00 0.00 3.67
3028 4495 6.049790 GGATTCGTCTGTCCTTATAAAAGCT 58.950 40.000 0.00 0.00 0.00 3.74
3067 4534 1.952296 GCTTTGATCAAGGATGGCGAT 59.048 47.619 20.77 0.00 32.37 4.58
3183 4650 6.909550 ACTGTTAAGAACTGTGAGAGATCT 57.090 37.500 0.00 0.00 41.25 2.75
3195 4662 3.766591 GTGAGAGATCTTGTCTTGAGGGA 59.233 47.826 0.00 0.00 37.29 4.20
3249 4722 9.559732 TGAATTCTACAGACAGAAGATCAAAAA 57.440 29.630 7.05 0.00 37.93 1.94
3344 4817 4.336433 TCAGGAGCAAGTCAGTTTTTCTTG 59.664 41.667 0.00 0.00 40.71 3.02
3654 5140 6.502136 TTGTAATGTGAAATCATAACCGCA 57.498 33.333 0.00 0.00 0.00 5.69
3808 5300 0.320771 GGTGACGTGGCAATCTGACT 60.321 55.000 0.00 0.00 0.00 3.41
3995 5505 2.936498 GGTAAGGATGGACATGACAACG 59.064 50.000 0.00 0.00 0.00 4.10
4121 5642 2.291457 TAGCCGCGCATAGCTGACAA 62.291 55.000 22.58 3.92 45.59 3.18
4134 5655 2.046283 CTGACAACAGCATGCTTGTG 57.954 50.000 25.78 23.15 42.53 3.33
4263 5784 8.315391 TGAGAGAAATAGTGAATTGAGTTGTG 57.685 34.615 0.00 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
286 304 2.546795 CGATAGTTGAGCCAAGGCCTAG 60.547 54.545 5.16 0.88 43.17 3.02
322 340 4.492791 ACGGTTTTAGAAATTCCCAACG 57.507 40.909 0.00 0.00 0.00 4.10
366 384 9.751542 AATATGTCGAAACATTTTACCAAAACA 57.248 25.926 0.00 0.00 43.74 2.83
665 693 8.854979 TGTGAGACAAAAGTAAACATGATTTG 57.145 30.769 0.00 3.87 37.10 2.32
677 705 7.823745 AAATAAGTCCATGTGAGACAAAAGT 57.176 32.000 3.83 0.00 36.68 2.66
681 709 8.783093 CACTAAAAATAAGTCCATGTGAGACAA 58.217 33.333 3.83 0.00 36.68 3.18
682 710 7.390440 CCACTAAAAATAAGTCCATGTGAGACA 59.610 37.037 3.83 0.00 36.68 3.41
683 711 7.606456 TCCACTAAAAATAAGTCCATGTGAGAC 59.394 37.037 0.00 0.00 34.31 3.36
684 712 7.685481 TCCACTAAAAATAAGTCCATGTGAGA 58.315 34.615 0.00 0.00 0.00 3.27
685 713 7.066284 CCTCCACTAAAAATAAGTCCATGTGAG 59.934 40.741 0.00 0.00 0.00 3.51
686 714 6.884295 CCTCCACTAAAAATAAGTCCATGTGA 59.116 38.462 0.00 0.00 0.00 3.58
687 715 6.404734 GCCTCCACTAAAAATAAGTCCATGTG 60.405 42.308 0.00 0.00 0.00 3.21
724 752 2.195567 TGTGCTCTGTTTGGCTGCC 61.196 57.895 12.87 12.87 0.00 4.85
754 782 0.540454 CGTCTAAAACCCTCCTCCCC 59.460 60.000 0.00 0.00 0.00 4.81
766 794 5.526115 GCATGTATAGCTACCACGTCTAAA 58.474 41.667 0.00 0.00 0.00 1.85
911 940 2.203877 TTGCCGGAGTAGGGTGGT 60.204 61.111 5.05 0.00 0.00 4.16
950 980 1.814793 GTGGAAGAGGAGTTTGGAGC 58.185 55.000 0.00 0.00 0.00 4.70
1055 1094 1.339727 GGTCACTTATGGTGGTGGGAC 60.340 57.143 0.00 0.00 45.38 4.46
1056 1095 0.988832 GGTCACTTATGGTGGTGGGA 59.011 55.000 0.00 0.00 45.38 4.37
1057 1096 0.991920 AGGTCACTTATGGTGGTGGG 59.008 55.000 0.00 0.00 45.38 4.61
1058 1097 1.405526 CGAGGTCACTTATGGTGGTGG 60.406 57.143 0.00 0.00 45.38 4.61
1059 1098 1.405526 CCGAGGTCACTTATGGTGGTG 60.406 57.143 0.00 0.00 45.38 4.17
1060 1099 0.902531 CCGAGGTCACTTATGGTGGT 59.097 55.000 0.00 0.00 45.38 4.16
1298 1361 1.924731 AGTGTCATCGTCTTGGAGGA 58.075 50.000 0.00 0.00 0.00 3.71
1322 1394 2.748641 ATCGACCACCCAGTCCCACT 62.749 60.000 0.00 0.00 32.91 4.00
1323 1395 1.838073 AATCGACCACCCAGTCCCAC 61.838 60.000 0.00 0.00 32.91 4.61
1324 1396 1.131303 AAATCGACCACCCAGTCCCA 61.131 55.000 0.00 0.00 32.91 4.37
1325 1397 0.392595 GAAATCGACCACCCAGTCCC 60.393 60.000 0.00 0.00 32.91 4.46
1326 1398 0.613777 AGAAATCGACCACCCAGTCC 59.386 55.000 0.00 0.00 32.91 3.85
1327 1399 1.405661 GGAGAAATCGACCACCCAGTC 60.406 57.143 0.00 0.00 0.00 3.51
1711 1795 0.174389 ATGTACTCGCTGACAGCCAG 59.826 55.000 21.55 20.28 45.67 4.85
1974 2058 3.242543 GCCGCACTGAGATTGTATCTTTG 60.243 47.826 0.00 0.00 40.38 2.77
2043 2127 5.281693 TGAACTGATGCACGTAATTTCTG 57.718 39.130 0.00 0.00 0.00 3.02
2072 2164 2.039084 GACAAGGACAGGAACCACTCAT 59.961 50.000 0.00 0.00 0.00 2.90
2226 2325 8.673251 ACATAAGAGGGAATCCTTAATTAGCAT 58.327 33.333 0.00 0.00 45.05 3.79
2310 2424 7.491682 ACTACGAGTTACTTTGACTAAAACCA 58.508 34.615 0.00 0.00 0.00 3.67
2349 2505 9.507329 AGATTAAGACAAAGAGTTGAATAGCAA 57.493 29.630 0.00 0.00 38.20 3.91
2382 3755 8.155821 TGATTAAAAACACGTCCATTCTTGTA 57.844 30.769 0.00 0.00 0.00 2.41
2383 3756 7.033530 TGATTAAAAACACGTCCATTCTTGT 57.966 32.000 0.00 0.00 0.00 3.16
2511 3886 8.779303 CCTAGAGTGCAATATCTATAGGATACG 58.221 40.741 14.56 0.00 43.95 3.06
2592 3969 5.427481 ACCCCTAATTAGAATCCTCACGAAA 59.573 40.000 14.28 0.00 0.00 3.46
2593 3970 4.966805 ACCCCTAATTAGAATCCTCACGAA 59.033 41.667 14.28 0.00 0.00 3.85
3183 4650 1.059584 TGCACCCTCCCTCAAGACAA 61.060 55.000 0.00 0.00 0.00 3.18
3249 4722 3.152341 CACATTTTCCACCAGCTCTCTT 58.848 45.455 0.00 0.00 0.00 2.85
3308 4781 3.317406 TGCTCCTGATGGATAGGCTTAA 58.683 45.455 0.00 0.00 42.29 1.85
3344 4817 4.157840 CCTAAAACCTGAAGTACCAATGCC 59.842 45.833 0.00 0.00 0.00 4.40
3519 5001 0.032540 TCGCTCGCACATAGATGCAT 59.967 50.000 0.00 0.00 46.47 3.96
3856 5348 1.424493 GCTCGTTCGGCTCAGGATTG 61.424 60.000 0.00 0.00 0.00 2.67
3995 5505 3.419759 CCGGTACTGCAACGCCAC 61.420 66.667 0.00 0.00 0.00 5.01
4066 5584 2.745100 TACAGCCGACGCTCGAGT 60.745 61.111 15.13 0.00 43.95 4.18
4134 5655 1.181098 AGCACCCAACATCAACTGCC 61.181 55.000 0.00 0.00 0.00 4.85
4263 5784 2.481952 CCTCAAGAAGTTAGTGTGCAGC 59.518 50.000 0.00 0.00 0.00 5.25


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

AutoCloner maintained by Alex Coulton.